A thorough analysis of the Fallout 4’s main storyline primarily focused on the main antagonist of the game as a character – an acting Director of the Institute, one of the game’s factions, solving their goals and personal motives while delving deeper into the suspicions the smaller part of the community held at that subject of the game’s story.

Fallout 4 is a game with many story inconsistencies, though, not as large as it first seems, with some of them being deliberate, others being a result of plain laziness at writer’s side. It is important to figure out which parts of the game’s story come off as intended and which ones are simple minor mistakes of an ingenious, one and only writer Fallout 4 has, elements of the game’s story one would not dare to look at as most of the game’s players are simply bored out of their mind or inattentive enough to figure out.

The Institute is the only truly antagonistic faction of the game that is led by a vicious lunatic that hates all of humanity. His faction shares no interests with the humanity on the surface, no moral fabric of any kind and prefers to replace the entire humanity with the synthetic robots, ultimately wiping everyone out and leaving the world a «perfect» place he envisions, with no real alive organism living on Earth. Everything is extremely simple, though unnecessarily tangled, as one of the human’s peculiarities is to believe in lies and be controlled by them, with knowledge being one of the lies he truly believes in, at the end with belief being his possessive power. What is told is not what is, that’s one of the characteristics being exploited by the Institute’s methods. The main character is a target that is being lied to throughout the game by many different individuals, ultimately nailing him in the coffin completely with the main antagonist stepping through the doorstep and claiming that he, the acting Director of the Institute is your son, as if the entire acting stage before that point wasn’t enough. Certain plot points allude to an extremely deliberate attempt to lie to the player who hasn't paid attention to the story, the ones that are buried behind overly simplistic dialogues of the game which gives the player a wrong idea on it’s story as a whole and keeps his attention from the fundamental answers that lie within the game. The story of the game isn’t as simple or dumb as an average player would think, not as smart either.

The Fallout 4 writer is a gingerbread man responsible for many things, those many things being the Skyrim and the Fallout 3. He was permitted to write all games developed by Bethesda after he had made friends with the industry legend – Todd Howard in the 90’s.























After he lost some weight and went on a diet he had established an even further empire at Bethesda Softworks ultimately becoming the «bestest» writer of the industry the world has ever known. Hated by many for his theoretical approach to writing, judging by a feedback received under the conferences he conducted, after throwing constant excuses at his laziness, put in simple terms, he sticks to the «why bother» story schematic, explaining that the modern player is unwilling to pay attention to the story and will, instead, make paper planes out of it. Another key moment revealed by him is that the Institute is inspired by James «Whitey» Bulger, a crime boss, guilty of many crimes. Primarily, the inspiration comes from him being a «monster in the closet, a mysterious unknown evil», he wanted to transport that into Fallout 4.

«The main fictional story is about an organization that is the monster in the closet».

«And so the Institute, in Fallout 4, is actually, James «Whitey» Bulger.»

He states that he drew upon his own experiences he leveraged from growing up, «those experiences of fear and suspicion». His explanation of the Institute heavily ties in with the personality of the main antagonist. Such an organization, especially as described by the Fallout 4’s writer would exploit anything to reach their goals and is, clearly, a one-sided organization. In order to figure out who the main antagonist truly is, one must go into details.

Player takes control of either Nate or Nora – the 2 protagonists of the game, with one of them dying and forcing one of the protagonists to continue the path into the wasteland that Boston ended up to be after a nuclear strike. Upon reaching the Vault all of the survivors along with Nate, Nora and their child are frozen in the cryogenic pods. When frozen, trapped inside a pod, Sole Survivor witnesses a terrifying event of the main character’s spouse getting killed by the Insitute’s agent, the second main antagonist of the game – Conrad Kellogg. Along with accompanying him Institute’s scientists, they are ordered to take a hold of the child and bring him the Institute, which was a successful mission. The life support for the other cryogenic pods was cut, leaving Sole Survivor the only survivor inside the vault. Exactly 210 years after the Great War, 10 years after the events of Fallout 3, in 2287, the main character is lucky enough to get thawed out all by himself, also due to the malfunction with the long time running pods. Sole Survivor finds himself in a difficult mental position left all by himself in the world he no longer knows, with the kid gone and the spouse killed. Making his way through many obstacles, mutants and ridiculous side-quests, rumor has it that the answer he’s looking for lies in Diamond City, getting there is now his primary target. The main character learns about the synths presence in the Commonwealth, robots manufactured by the Institute, operating from the shadow and infiltrating Commonwealth societies. Making his way through more ridiculous side-quests for hundred hours he finally, or even possibly, reaches the Diamond City, the most prestige and regulated settlement in all of Commonwealth.







The main character is forced to make an errand making his way to the detective agency. Lied to by many individuals and synths, even by the city’s major himself, who is a synth, main character ends up at a detective agency. A synth detective - Nick Valentine finally greets him, but not in the detective agency, instead, in some Vault on the other part of the map where he is trapped and in need of assistance that only the Sole Survivor can give him. Finally escorting him back to the Detective Agency, the main character is questioned and the information about Kellog’s potential whereabouts is revealed by Nick Valentine. His potential whereabouts are exactly at the same city, just one slummy house after the other away. Surprisingly, he isn’t actually there and upon searching the house for clues as to where he might be, later with the help of the dog companion – Dogmeat, trace leads up to Fort Hagen, a base of operation for Kellogg, originally a military command facility. A talk with Kellogg reveals unexpected sensitive information – his son is at the Institute. Retrieving the cybernetic brain augmenter used to access Kellog’s memories, a mandatory augmentation equipment that had to be installed into his hippocampus so that later, the Institute could see what he was up to, Sole Survivor views his memories at the Goodneighbor’s Memory Den, located in the harsh city full of triggermen and corruption.

Sole Survivor finds out about Brian Virgil – an escaped Institute scientist that managed to run all his way into the Glowing Sea, a heavily contaminated and exposed by radioactive radstorms part of the Commonwealth. Infecting himself with a unique strain of FEV to survive in harsh conditions, he is now spending his time in the cave. The player is directed to find an Institute Courser’s chip, bringing it for a decode to the Railroad, an underground secret society trying to free synths. After that, Sole Survivor receives a blueprint from Virgil, the one that would help build a device picking up a molecular relay frequency and transport the player to the Institute. Ultimately, reaching the Institute, at the lower levels of the facility the Sole Survivor meets his son locked behind a cell. He now believes that the Institute’s Director is his father. The main antagonist, the Director reveals himself, «shuts down» Shaun using a code phrase and now claims to be Sole Survivor’s true son, confusing the main character and putting him at an irresistible emotional disadvantage. Not knowing what to do next, even the player’s choice does very little to influence your main character, as he is confused by a warm welcome, the new information and a moral brick wall. From that point of the story, the player character is now able to join the Institute or destroy it with one other faction he had established a good relationship with. The last player’s choice puts the main character at a dilemma as to whether he should take a 10-year old son who, as Sole Survivor learns is a synth or leave him for dead. Certain inconsistent story elements require the player to figure out the information given to him prior, that is, if the player is willing to gather and use it.

The Commonwealth is a ruthless place. A wasteland with long forgotten values with the major population being mutants, fanatics, raiders and Gunner mercenaries is now corrupted by the synths, slowly exterminating all of humanity from the shadow. Only the Minutemen, enthusiasts trying their best to protect people from any threat in existence could sort the mess out if the player decides to rebuild them, while Brotherhood of Steel is the faction that takes what doesn’t belong to them, establishing martial law and the base in any place they visit, American military style. It is the player’s choice if he wants to make safety rebuilding weaker faction from the ground up or succumb to evil parasites of the Commonwealth, factions, the goals of which don’t put people as a top priority. Regardless of the player’s personal choice at factions, there are always lies everywhere.

Lies and the confusion is a primary context on what the narrative of the game is built on, the mystery behind who is a synth, where the Institute is located, choices with equally undesirable outcomes as the player is engaged into it’s narrative, is learning more information on the state the Commonwealth is in and whether synths are to be trusted. The player has to gather evidence to figure out if the human standing next to him is a synth and if there is no true alternative, the only way to receive an answer would be killing him and checking if there is a synth component. Ordinary citizens are tangled into the paranoia as they’re afraid of being replaced by a synth, their close relatives suddenly turning on them and with the synths sent to infiltrate the societies and gather information, ordinary men could not take any chances.

Throughout the game, the Sole Survivor is being lied to many times. Misled by the whole town of the Covenant, the Mayor of Diamond City, lied to by the strangers on the sidewalks trying to scam the player or lure him into the trap, impersonator of Preston Garvey from the Commonwealth Minuteman roaming the streets, Bobbi orchestrating a Big Dig and luring the player with fake information, betrayed by characters such as Theodore Collins and many more.

One of the lies stands out.

Deacon, a Railroad agent, gathering intel for the faction all around the Commonwealth with an unclear past can be acquired by the player as a companion. He has a tendency to spy on people around the Commonwealth, gathering as much information as possible, working undercover in different organizations. The main subject of his attention is Sole Survivor, soon after being released from the vault, unbeknownst, he is being followed by Deacon throughout the game, wearing different disguises. Hiding in plain sight, he knows of all the legendary adventures the Sole Survivor has been through and upon reaching the Railroad for the first time, his dialogue changes drastically in correlation to all the events he lived through in the wasteland.






















Later, as a companion, in depends on the affinity, more information is known about the character and his personality traits. He is constantly playing tricks on the Sole Survivor, admitting that most of the things he’s telling him, other people, is a plain lie.

Deacon: «Whether the Institute's motivated by vengeance or faulty intel, it doesn't matter to the people left behind. It doesn't matter much to me. I'm a synth. At least that's what they tell me. So I really don't have anything to lose.»

Sole Survivor: «You're a synth? Why didn't you tell me before?»

Deacon: «I don't like talking about it. I was one of the first synths they did the whole cranium reboot on. So it was a bit of a botch job. Most synths have fun fake memories. A happy home, a family. Me, I got nothing. And that... well, it does something to you. Since we're traveling together I want you to take this. It's my recall code. If you ever need to know something about the Institute, read it to me.»

Sole Survivor: «If you expect me to believe you, I want proof.»

Deacon: «Alright, you got me. No fooling you, huh? Don't take it personally, I lie to everyone. I'm supposed to be showing you the ropes in the Railroad. That code I gave you is a hard truth. You can't trust everyone.»

Deacon uses lies to educate the player that you can’t trust everyone, even if they sound sincere. He is revealed to be a human being, if killed by the player, as no synth component is found.

Deacon: «We've been making the rounds, doing the job. It's time you learn the Big Secret. Everyone thinks that Desdemona is the big boss. She calls the ops, gives the ra-ra speeches. But it's just an act. She does what I tell her to because the Railroad's my show. It's been that way since I founded it.»

Sole Survivor: «You founded the Railroad?»

Deacon: «Me and Johnny D and Watts. That was 60? 70 years ago? After awhile you lose count. I tell everyone I get the occasional face change to stay anonymous. Truth is, it takes a lot of work to keep this mug handsome.»

Sole Survivor: «You've lied to me at least once. This is just more of the same.»

Deacon: «Yeah, you got me. But you're going to hear the same sort of lies elsewhere. There are other organizations out there. And, in time, I'm sure they're going to spoon-feed you their own patented form of BS. Ignore the verbage and look at what they're doing. What they're asking you to do. What sort of world they'd have you build and how they're going to pay for it. And at the end of the day you'll need to make a choice. Make it the right one.»

Deacon warns the player about the questionable ideologies of different factions that don’t fall in line with their actions, foreshadows that eventually, the Sole Survivor will be lied to, as anyone would want to have «the most resilient man in the Commonwealth» on their side. Him changing faces is the truth, Deacon was already kicked out by the former Railroad HQ Leader, as he had spent a month as a ghoul. Face surgery is much more common in the Fallout universe, doctors are capable of performing complex operations, changing faces, even the skin color. Deacon, also, was not the one who founded the Railroad, they have a clear hierarchy in their faction, he also isn’t that old.

It isn’t known when the Railroad was truly founded, but certainly not 60-70 years ago. The generation 3 synths resembling human, back then, were believed to be practically new, if they existed at all, at that time, not many synths would escape and they were only rumors, while the very first prototypes of Gen-3 synths that didn’t look human, known to be DiMA and Nick Valentine weren’t in any way involved with the Railroad. Railroad is known to have existed in 2266 when it’s old management was broken down. Desdemona, the current Railroad leader, only signed up around 2276, a year before the Fallout 3 main events and 11 years before the Sole Survivor got thawed out, while the other Railroad HQ members along with Glory and Tinker Tom seem to have too, joined the faction fairly recently. The Railroad history is underdeveloped, which makes most of it’s information a mystery and judging from the information acquired during the side-quests of Fallout 4 «Dr. Roslyn Chambers found, no medical tests or procedures can identify someone as a synth without killing them» which confirms that the Railroad was originally founded based on simple rumors, as they had no chance on identifying who was a Gen-3 synth even if they did exist. Railroad tells Deacon that he is a synth, as he keeps lying about having no recollection of his former self, which is not true, as the faction was always purely based on speculations and Deacon tells the Sole Survivor about his history, if affinity is at maximum.

Deacon: «I ran with a gang in University Point. We called ourselves the UP Deathclaws. For kicks we'd terrorize anyone that we thought was a synth. We kept egging each other on. Started with some property damage graduated to some beat downs. Then, inevitably, a lynching. The Claw's leader was convinced we'd finally found and killed a synth. Looking back, I'm not so sure. That one was enough for me. It was his eyes... Those eyes haunt me. Bulging. So I turned my back on my "brothers" - broke all contact. Time passed, I became a farmer, if you can believe that. Then one day I found someone. She saw something in me I didn't know was there. Barbara, well, she was... She just was. She had a smile like on those old magazine covers. Her eyes... We were trying for kids, ekeing out a living. Then one day... It turns out my Barbara... She was a synth. She didn't know that. I certainly didn't. I don't know how the Deathclaws found out. But... there was blood.»

Not only that, for the Railroad, identifying who was a Gen-3 synth was impossible, but «lending a hand» and protecting Gen-1,2 synths, with them being hostile would be pointless and out of the question, they don’t even have personality. The only conclusion to make is that the Railroad, at it’s early days, was «helping» anyone they could, believing and telling certain individuals in danger that they’re a synth, deceptively attracting them to their cause. Many Gen-3 synths have no recollection of actually being a synth, since they’re memory wiped by the Railroad. The Railroad practices, over the years, leading up to the events of Fallout 4 have proven to be unsuccessful, judging by how little members of the faction there is left, possibly because back in the day, the Railroad faction was an ever bigger fraud when led by 2 other mentioned-only, unseen leaders – Agamemnon and Pinky Thompson, who both had to leave the office. With the questionable ethics, Railroad is a dead end.

The Broken Mask Incident is a rumor going around Diamond City about an incident involving one synth massacring the market bar of the city. The incident is believed to have taken place nearly 60 years ago, in 2229. It implies that one day, a man known as Mr. Carter came to the city and claimed he was out from west. Gathering residents around the bar counter, he shared stories about the state of the Commonwealth, putting an impression on the city’s residents. Suddenly, when he overindulged with the several drinks, his smile faded, his cheek began to twitch and Mr. Carter, pulling a revolver out killed the bartender to the head, after that, executing few other residents. He was killed by the security and the inspection of his corpse revealed plastic and metal, confirming that he was a synth, indistinguishable from human, the one they’ve never seen before. Such event pushed Diamond City for nearly 60 years of constant paranoia. The only eye-witness old enough to remember the incident is Eustace Hawthorne, living in Diamond City during the events of the game, who shared the story with Piper Wright, a city reporter, constantly raising paranoia even further, up until she was banned from the city by the Mayor.

Regarding the incident, it is later revealed in the «Director’s Recording #108» that this was just a prototype synth that escaped the Institute. It was not ready for testing and wasn’t authorized to leave the facility. The recording also confirms that at the time of the incident, the Institute was under command of a female Director.

Right after the incident, in the 2230s a «Commonwealth Provisional Government Massacre» occurred. At some point, various settlers have stood up and decided to establish a regional government in the Commonwealth. During an important meeting, to which each settlement’s representatives were sent for the agreement discussions, one of the Institute’s representatives – a synth, killed everyone at the meeting, ultimately preventing all attempts to form such a government.

This event was the last straw that completely tore down all possible trust for the Institute, from that point they were deemed hostile. Suspiciously, right after those events, it was dead quiet for decades and no further incidents ever happened.

The timeline of Broken Mask incident and CPG suggests that the Railroad wasn’t actually founded 60 years ago, in the 2220’s. It’s never stated in the actual story, apart from Deacon’s lies of it being founded «60-70» years ago. All it is, is just a hint towards a bigger plot inconsistency. This was the time when the Gen-1 and 2 synths were roaming around the Commonwealth in low amounts and Gen-3 synths that would be indistinguishable from human weren’t known to anyone, apart from Broken Mask incident at the end of that decade. That synth, however, was a malfunctioning prototype, suggesting that they’ve never truly achieved the goal of creating a stable synth at that time. The CPG massacre eventually left a scar of fear and paranoia for decades, but because no major events occurred for nearly 50 years suggests that the Gen-3 synth development has had a major breakthrough only during the events of Fallout 3 and never before. At that time, only the first true advanced synths were created and held on a leash by Dr. Zimmer in Washington, as he constantly tells the player about the breakthroughs done back in the Commonwealth. The Institute wasn’t able to create a properly functioning synth for 50 years, which is evident by the events. The earliest event that ever happened in Railroad and is mentioned in Fallout 4 dates back to 60’s and without being able to identify who is a Gen-3 synth without killing them, only just a few prototypes at the time of the incidents could ever manage to escape the facility. Establishing a Railroad to have no Gen-3 synths in the 20-s and 30-s cleared for the surface, especially their existence, at the time, being nothing more but a mere rumor in some parts of the Commonwealth, would be completely irrational, they wouldn’t have synths to operate on, not to mention that the largest influx of Gen-3 synths is known to have happened only during the events of Fallout 4. The Railroad was founded very late and not how it is initially believed. It is also believed, that Shaun was kidnapped 60 years ago and not only that there are big plot inconsistencies that suggest otherwise, but the Gen-3 synths that are malfunctioning at that time couldn’t derive from Shaun’s DNA. Such operations would only result in his death, on infant especially. The synths don’t work as intended during the Broken Mask and the CPG simply because, as stated by the main antagonist, they had an irradiated DNA, the Shaun, however, didn’t, which answers that Shaun wasn’t actually kidnapped back then, as the breakthroughs would have been done much earlier if that was the case. Why was synth Shaun in Fallout 4 created in the first place? The main, important plot point that tends to be missed, is that synths aren’t clones, it is impossible to clone a man and have two people alive and present. When human subject is kidnapped – the original dies. And if Shaun was truly kidnapped 60 years ago, wouldn’t an infant, especially, when the Institute is only exploring new ground at synth research, be killed during an experiment? Was the Shaun kidnapped for an entirely different reason? There are many more inconsistencies that answer a load of questions as to why the timeline is entirely different and the events aren’t what they seem to be.

Conrad Kellogg is a mercenary ended up in the Commonwealth, turned an Institute agent. He is one of the antagonists of Fallout 4.

At the beginning of the game, along with some Institute scientists, he is seen killing the spouse of the main character and taking the kid. That stresses the main protagonist to go out and look for his son. Kellogg, in the game, is the source of many answers. When first confronted by the main character, he tells the player more about the information he’s looking for.

Kellogg: «And there he is. The most resilient man in the Commonwealth. Funny, I thought I had that honor.»

«Your son, Shaun. Great kid. A little older than you may have expected, but I'm guessing you figured that out by now. But if you're hoping for a happy reunion? Ain't gonna happen. Your boy's not here.»

Sole Survivor, in his quest for searching his son has made a lot of noise in the Commonwealth. From clearing raider settlements to meeting with key figures he has made a name for himself. At that time, Kellogg himself believes that Shaun is just a kid and is a «bit» older.

Kellogg: «Shaun's a good kid. A bit older than you expected, am I right? But he's doing great. Only... he's not here. He's with the people pulling the strings.»

Kellogg does not believe that the «Father», the Director of the Institute is the main character’s son. He believes that the son he’s looking for is 10 years old and is currently held at the Institute by the «people pulling the strings». If it would have been truly his son, it would not be the Director. He states that both the main character and Kellogg is a puppet. A 10-year old boy synth, throughout the game, is used as a decoy for the main character.

Kellogg: «Shaun's in a good place. Where he's safe, and comfortable, and loved. A place he calls home. The Institute.»

«In another life, you probably would have been a good father. But here... in this terrible reality? You just don't get that chance. I admire your dedication to fatherhood. Even if it is ultimately useless.»

When killed, player discovers that he was augmented with the «Cybernetic brain augmenter», an implant making it possible to access his memories. Taking it to Goodneighbor’s Memory Den, he contacts Doctor Amari, she helps people relive their past memories. Host is connected to a lounger’s network, sealed in a pod, as he is taken in for a memory trip. A clear explanation of it’s function algorithm is described by Amari herself:

"Don't bother asking me about how the Memory Loungers work. I don't have time to teach the years of neural physiology it would take to understand."

Both the Sole Survivor and a synth Nick Valentine are connected to the memory loungers. Synth serves as a host, while the main character is a viewer of Kellogg’s memories that move in an interconnected parallel between the two entities.

Nick Valentine: «If I start cackling like an old, grizzled mercenary, pull me out, okay?»


The Sole Survivor then moves through the «intact memories» of Kellogg, observing his earlier self as just a kid to a full-head cyborg mercenary as an Institute asset. The most important bits of his memories that answer some of the questions lie during his first contact with the Institute, his involvement with it later on.


The first involvement with the Institute is shown by him «taking a job» at the Institute. Proving his worth as a valuable asset to the female employer by showing off his combat skills right in the same room, eliminating all synths there and then, he is then applied to do work for the Institute as a surface operator. It isn’t known whether the female employer is the Institute’s Director at the time of the first contact, as her name, in the subtitles is the «Institute Agent». Her being a Director might add up, if not for the story intricacies made later on. There are multiple main Institute figures in a sub-faction: a Directorate that consists of the multiple directors each responsible for something different. The player is then taken to another intact memory, the most critical one.

Amari: «We're running out of brain here... uh... ah, there's one that looks mostly intact. Connecting now.»

That statement possibly refers to a high leap between the events, suggesting that the vault assignment took place a significant amount of time after his initial meeting with the «Institute Agent». That «intact memory» takes the player back to the cryogenic pods of the vault, where he is now able to move around and interact with the Kellogg’s memories. It is believed that such even took place as far as 60 years ago from the main story events.

Kellogg: «I was now the Institute's main operator in the Commonwealth. If they needed something done, they came to me. It wasn't usual for anybody from the Institute to come along on a mission. So this one stood out.»

All the main Institute’s surface operations are now carried out through Kellogg. It is highly possible that Kellogg underwent many assignments, it might have taken a few years for him to become the «main operator», judging from the statement of him becoming one when around the cryogenic pods. It isn’t known whether there were other operators of different ranks in the field, but that might definitely be the case. When promoted to the «main operator», he is tasked with the most urgent mission to carry out, the one so important, that he was sent to the vault with the several scientists accompanying him.

«I didn't know then who it was we were grabbing from the Vault. Of course, neither did they. Not really.»

Referring to a typical «need to know basis» schematic. Neither the Kellogg or scientists knew what was the purpose of that kidnapping, none of them were even briefed beyond the very basics of information. At that point however, what he is actually referring to, is that at the time of kidnapping, because the main information was classified, he couldn’t even guess who it might be that they were grabbing from the vault. They were, infact, grabbing the Institute Director’s son he always wanted…

«I never knew why we didn't just refreeze the rest of them, but we had our orders. I guess the old man didn't want so many loose ends. Too bad he left alive the one person he shouldn't have.»

This is the most important bit of Kellogg’s memory that directly confirms the key story element – the mission was planned and assigned to Kellogg by the Institute’s Director no other than the «Father» himself. The orders were very specific, they involved taking the kid, cutting the life support for all other vault subjects, which was successfully done, as they would be loose ends if thawed out, could potentially cause a lot of problems. What wasn’t actually successful is the «collateral damage» Kellogg created by killing the spouse of the main protagonist. The Institute was planning on having a «backup» that is the son’s parents, get their DNA instead, but only if the experiment on Shaun would be a failure, which was a success and the Sole Survivor was never touched. The main character being a backup is confirmed by Kellogg, which was the first ever phrase he directed to Sole Survivor: «At least we still have the backup...»

Because the Sole Survivor was left alive, as ordered by «Father», he created problems for Kellogg and himself without suspecting he would go as far as to reach the Institute.

Kellogg: «Even then, I knew it was a mistake leaving him (spouse) alive. I understood that kind of revenge, no one better. But I was cocky enough to assume I could handle some soft prewar Vault dweller, even if he somehow got thawed out. At least I know those Institute bastards will soon get what's coming to them, too.»

Kellogg expected an easy battle if confronted by the Sole Survivor, if it was to ever happen, but he did suspect it might happen as a revenge. He knew it was a mistake leaving him alive, even if ordered to do so. The Sole Survivor gets thawed out by a pod malfunction, possibly due to the heart palpation and the temperature the body generated at some point, the same malfunction that happened with the pod C3.

«I'm glad I didn't have to kill the kid. I'm not saying I haven't done it, but I never like to.»

Not much is known about Kellogg’s past, though that statement might be much more connected than it first seems. It might suggest that he technically did kill Shaun by taking him to the Institute, eventually, when he was experimented on, his DNA was taken, leaving the kid dead.

The player is then taken to the last intact memory that appears to be the recent one.

Amari: «Is that... your son? This appears to be a very recent memory, so... good news, I think.»

This memory is, indeed, recent. The Diamond City radio is heard upon stepping in with the same awkward host – DJ Travis, as he covers the latest addition of «Publick Occurrences» newspaper.

Kellogg is seen sitting on the chair, looking after Shaun.

Kellogg: «This whole setup in Diamond City was part of some elaborate plan of the old man's. Seems obvious now that we were bait for our friend from the Vault. The timing couldn't have been an accident. That's not how the old man works. I wonder if he outsmarted me in the end. Another loose end tied up.»

The «Father», Institute’s Director now uses Shaun as a decoy so that the Sole Survivor and Kellogg confront each other. At that point «Father» doesn’t truly believe the Sole Survivor will manage to kill the highly-trained mercenary and with all hopes doesn’t want that to happen, as at that point he is desperate. Kellogg, once again, wasn’t told a thing, which is why he had his suspicions.

«It wasn't my idea to settle down with the kid in the middle of Diamond City. I thought it was a terrible idea, actually. But it was one of the old man's pet projects, so here we were. Me and the kid like a happy little family.»

Ordered by the «Father» to settle in Diamond City, where the Sole Survivor is aimed to go, he is forced to reside in the city with synth Shaun being a decoy. It is important to notice that he refers to Shaun as a «pet project», not to the synth and the like. Synths don’t fit the label of a «pet project», the real living organism, however, does. The reason being, Kellogg knows that only 10 years had passed and Shaun, potentially, was growing naturally behind his back, him calling Shaun an old man’s «pet project» confirms that he thinks that «Father» is not related to the kid he kidnapped from the vault, he would phrase that differently, he thinks that synth Shaun is the real version of the kid that is being experimented on at the Institute, except he doesn’t suspect him of being a synth and the real Shaun, possibly, dead. The reason he calls him an «old man» throughout the years is because he has no respect towards «Father», calling him that wouldn’t fit Kellogg’s character.

«I ended up kind of liking it. A reminder of what my life might have been if things had turned out differently. But there's no going back. I knew it was just temporary, and it would be back to normal business before too long.»


The Institute Courser then unexpectedly steps into the room making Kellogg reach for the trigger before he recognizes him.

«One of these days you're going to get your head blown off, just barging in here like that.»

If accessed, Kellogg’s memory on the courser raises more questions and suspicions:

«The new breed of synths could easily pass as human. Some of them did. But the coursers - they weren't built to blend in. They were killing machines, pure and simple. Smarter, stronger, and faster than almost any real human. I'm just glad they were always on my side.»

Interestingly enough, Kellogg states that easily passable as human batch of synths is new, divides coursers and Gen-3 synths. That would only confirm the initial suspicions of the Gen-3 synths being nothing more than underdeveloped prototypes for many decades, even 60 years ago, but what it also confirms is that the Gen-3 synths the Sole Survivor is seeing in the Commonwealth are completely new, which means they couldn’t derive from Shaun’s DNA 60 years ago. It wouldn’t take them many decades to create a stable synth when they already have a non-irradiated DNA sample, the Incidents, involving malfunctioning synths at that time, also wouldn’t have happened.

That would only suggest that the major breakthroughs were done as little as 10 years ago, Shaun was too, kidnapped 10 years ago, which also adds up with the Shaun’s age seen in Fallout 4, as well as certain inconsistencies brought into the story with the player’s arrival to the Institute facility.

Courser then tasks Kellogg to eliminate Dr. Brian Virgil, a scientist that had escaped the Institute due to the guilt he gained after experimenting on real humans, using FEV to create super mutants.

X6-88’: «We know he's hiding somewhere in the Glowing Sea. Here's his file.»

Kellogg: «Wow. Some heads are going to roll for this. Capture and return or just elimination?»

X6-88’: «Elimination. He was working on a highly classified program.»

Kellogg: «So... I guess you're taking the kid back with you.»

«If anything like this had ever happened before, I'd never heard of it. Maybe a sign that the old man was losing his grip.»

«Father» is very urgent at sending Kellogg to kill Virgil, as he could help Sole Survivor reach the facility, this is something he doesn’t want, but the Kellogg is stubborn and wants the Institute to «get what’s coming to them» instead.

Both Shaun and courser teleport back to the Institute which roughly provides the Sole Survivor with an idea on how to get to the facility. The entrance to the Institute is teleportation, it has no direct, open entrance. At that, Sole Survivor acquired enough information and is now headed to Glowing Sea.

Upon meeting Virgil, the Sole Survivor knows of an instrument that can help teleport him to the Institute facility, he is then sent to retrieve a courser chip and with the help of the Railroad’s Tinker Tom the chip is decoded and the frequency code for the molecular relay device that can be used to access a facility is obtained. Once the device is built, Sole Survivor powers it up, and teleports directly into the Institute facility. From that point onwards, the most important information in the story is revealed.

Clean white corridors, safe from radiation environment, no mutants, friendly at first look faces doing their job and the warm welcome are the first things Sole Survivor experiences upon reaching the facility. That is, after he actually reaches the elevator through the terminal room. The evil lies in details.

What the Sole Survivor first hears is the «Father» welcoming him on the speakers and takes him on a short tour to the elevator. From there he is seeing the size of the facility, the trees growing, separate sectors and the people of the Institute.

«Father»: «Hello. I wondered if you might make it here. You're quite resourceful. I am known as Father; the Institute is under my guidance. I know why you're here. I'd like to discuss things with you, face-to-face. Please, step into the elevator.»

The «Father» now tries to impress the Sole Survivor, tells him an already prepared script. He tries to come off as friendly to the needs of those, on the surface, even though he is the one responsible for most of the threats done to the Commonwealth and to the Sole Survivor himself.

«I can only imagine what you've heard, what you think of us. I'd like to show you that you may have... the wrong impression. Welcome to the Institute. This is the reality of the Institute. This place, these people, the work we do. For over a hundred years, we've dedicated ourselves to humanity's survival. Decades of research, countless experiments and trials... A shared vision of how science can help shape the future. It has never been easy, and our actions are often misinterpreted by those above ground. Someday, perhaps, we can show them what we've accomplished. But for now, we must remain underground.»

Fallout 4 shows that the «science» replaces what it means to be human and is the cause of most of the catastrophes done to all of humanity due to the naïve perceptions of the «scientific» eggheads working for the so-called «benefit of all». That however, throughout the history was always done for fame, pocket and the cult of personality amongst the friends of those, in specific societies that let the deception happen at a common interest. Deception of humanity is also a common interest of the Institute in the game.

The whole of Commonwealth is at a growing paranoia because of the threat that is the Institute, as their intentions aren’t clear to anybody, apart from them trying to build a fake «perfect world» with just the synths and no human in existence, that is exactly what they’re trying to do. All the research did not go for the benefit, all went for a questionable ideological view, a dream and a complete delusional nonsense spouted by an old man that is the «Father» as an excuse to destroy the world before he dies. The «scientists» working inside the Institute themselves don’t understand the consequences of such actions, they’re the simple fanatics that ignore all moral and that subject as a whole if brought up by the characters in the game itself. Fallout 4 doesn’t depict the Institute as a faction that tries to help the humanity, they do quite the opposite by creating synths and experimenting on humans to create super mutants to then release them in Wasteland for them to chew everybody up. Regardless under what deception they disguise their true purpose, it’s nothing but anti-human and consequences of their actions serve no benefit for humanity, viewing them as anything beyond that is plain moronic, especially by how one-sided the faction is in the game.

The Institute puts and knows no limits. When in the elevator, the Sole Survivor observes the labs and the «Father» tries his best to impress him with nothing but empty words and a «breathtaking» view, attempting to blur the evil that lies in their intentions, an equivalent to burning the whole city and telling the next person of how beautifully lit up it all is. Most of the Institute’s experiments are failures, as for decades they kept producing malfunctioning synths, as they had no clean DNA, also countless failures in experiments on living subjects. They have accomplished nothing but destruction and all of these toys will eventually be gone, which is why they’re afraid of the surface.

«There's too much at stake here to risk it all. As you've seen, things above are... unstable. I'd like to talk to you about what we can do... for everyone.»

Meanwhile there is no trace of them doing anything for the humanity and never will be even in words of the «Father». Even when confronted by the Sole Survivor, he’ll do a poor job at making up what the Institute actually does for anyone.

«But that can wait. You are here for a specific, very personal reason. You are here for your son.»

The «Father» knows what the Sole Survivor is there for and the next thing he does is teasing him with the synth Shaun as an emotional exploit to then quickly strike and use his weakness against him, as the Sole Survivor is left confused.

The next thing that the Sole Survivor is seeing is Shaun who is believed to be a synth. Shaun doesn’t recognize the main character and screams for his father.

Sole Survivor: «Shaun, it's me. I'm... I'm your dad.»

Shaun: «Who... Who are you? Father? Father! Help me!»

The «Father» steps into the room, uses a recall code and shuts Shaun down.

«Father»: «Shaun... S9-23 Recall Code Cirrus.»

«Father»: «Fascinating.... but disappointing. The child's responses were not at all what I anticipated. He's a prototype, you understand. We're only just now beginning to explore the effects of extreme emotional stimuli.»

Here comes the very first batch of lies. That statement is extremely inconsistent to the point of being contradictory to everything he says after that and to everything synth-related that was seen before. The Sole Survivor walked a long way to the Institute, through the whole Commonwealth meeting all kinds of people and most importantly synths. All the new synths he sees in the Commonwealth are very emotional and tend to deny being a synth. Even decades ago when one of the malfunctioning synths escaped the facility during a Broken Mask Incident he was charming and emotional to everyone in Diamond City, that’s not even counting earlier synths that is Nick Valentine and DiMA. A player attentive enough would instantly know that’s just a lie. Wouldn’t an «emotional stimuli» happen much earlier if they had real technological breakthroughs 60 years ago? That is just a simple lie to distract the player, as synths were always emotional.

«Father»: «Let's start anew. I am Father. Welcome to the Institute.»

Right off the bat, it is important to clarify that the «Father» is not Shaun. In order to get a rough idea of who he might actually be, an earlier Kellogg-related event should be referenced. One of the holotapes of the game found at the Institute gives the player an intel on how Kellogg received his augmentations:

"Institute Scientist": "Just keep talking if you can... I'm afraid this may be rather painful."

"Kellogg": "Don't worry about it, doc."

"Institute Scientist": "Anesthetic would lower your blood pressure too much, and I need you to remain conscious."

"Kellogg": "You already explained all that. It's going to be worth it, right?"

"Institute Scientist": "Oh, most definitely. These implants are much more advanced than anything you've had before. Doctor Walter is very pleased with you. The Gen 3 synth program is finally making progress, thanks to the genetic material you recovered."

"Kellogg": "You're talking about that kid we got from the Vault?"

"Institute Scientist": "Yes, a perfectly unspoiled DNA sample! Now this next part is especially delicate, so if you can please look straight into the light..."

"Kellogg": "Should everything be purple?"

"Institute Scientist": "Hmm? Oh that's just a calibration error... how about now?"

"Kellogg": "Better."

"Institute Scientist": "I'm just glad to have a chance to test these on a cooperative human subject. Normally the directors are very touchy about allowing this kind of technology outside the Institute. They must find you extremely trustworthy."

"Kellogg": "You're sure these are going to work, right doc?"

"Institute Scientist": "Oh, yes. When I say "test" I simply mean collecting data over time, which will be very valuable to making further improvements. This next part may be exceptionally painful. Try your best to remain conscious."

Most of the Institute «scientists» seen in the facility were referenced one way or another before or after the Sole Survivor’s arrival. Doctor Walter, however, is a name that comes from nowhere. He is believed to be the leader of Gen-3 synth development and might be very person who sent Kellogg to retrieve a child. It would be much more fitting to put someone such as him in place as a Director and if he was the one behind the Gen-3 synths, then he will, without a doubt, be called a father of Gen-3 synths. The «Father» might actually be Walter himself, that’s how synths and everybody around came to know him, not for the reasons he tells the Sole Survivor. The real progress on Gen-3 synths was achieved 10 years ago when the Shaun was kidnapped.

Sole Survivor: «Father? That's your name? Your title?»

«Father»: «Father is my unofficial title. It's what I've come to mean to the people of the Institute. Just as... As you mean to your son. To Shaun.»

During that replica, his voice seems to make a lot of pauses, minor stutters, as he continuously improvises and makes things up as he goes, at all times doing parallels with Shaun, his voice direction is very deliberate and so are the facial animations at different times, at places pretending to be sad or being actually fascinated if the lies on Sole Survivor worked. The reason of him not being able to speak about Shaun easily is because of the possible fact that the real Shaun is dead and Sole Survivor, as a parent would experience a high amount of pressure and anger if provoked with the truth. Instead, «Father» finds a way to squeeze his lies in about being his actual son, which doesn’t realistically make any sense, but that would put his questions to rest and attract him to their cause. During all of that Sole Survivor is confused and there are a small amount of options to choose from due to his current mood.

Sole Survivor: «This is... insane. All of it.»

«Father»: «The degree of trauma you're experiencing right now is understandable... Please, just try to relax. I know this is all difficult to take in.»

«Father» speaks that as he reaches out his hand, a gesture that in that instance would mean him not wanting the Sole Survivor to lose his grip, for it to not end in a bloodshed, as the Institute would not be able to contain and kill him.

«Father»: Ah, levity. Excellent. A sure sign that you adapt quickly to stressful environments.

If player picks a sarcastic option he knows that he succeeded at taking Sole Survivor’s trust, he would be a great candidate for Director’s spot and because he’s not too much critical of the situation it would be easier to pull him in to their side. A fruitcake like that is exactly who he wants to work with, just like the rest of the Institute.

Sole Survivor: «Just... Help me understand what's going on here.»

«Father»: «I promised answers, and answers you shall have.»

Answers is exactly what the Sole Survivor gets, at the expense of truth that is.

«Father»: «But... I need you to realize that this... situation... is far more complicated than you could have imagined. You have traveled very far, and suffered a great deal, to find your son. Well, your tenacity and dedication have been rewarded. It's good to finally meet you, after all this time. It's me. I am Shaun. I am... your son.»

«Father» constantly reminds the Sole Survivor of how far he went and how much he has seen throughout the whole dialogue, his trauma is exactly what the «Father» is taking advantage of with the additional lies of him being his son, that way he’ll stop any further attempt of Sole Survivor to look for his son anywhere, he’d rather spoon feed him a lie. It is important to add that the «Father» has no documentary confirmation of him being Shaun, despite «records» somehow, out of nowhere being discovered about the vault, instead he offers the Sole Survivor empty words while hiding his true identity under the «Father» label. His lies are so carefully planned that he hid all the sensitive information and uses Sole Survivor as a candidate for the Director role, it’s critical for him that no one around him would know it’s just a ploy and an experiment. There are no records of «Father» being Shaun, even in holotapes referencing synth Shaun.

Sole Survivor: «BS.»

«Father»: «Is it? After all the things you've seen and experienced in the Commonwealth? Think about it...»

Anything that has happened on the surface has nothing to do with him even remotely being related. The reason «all the things» is referenced, is for the sole reason of him stopping his search for Shaun and if the outside world caused much harm to the Sole Survivor, he thinks it would work to attract him with a lie instead, that’s why the «Father» constantly reminds him of Commonwealth. Everything that has happened in the Commonwealth would make the Sole Survivor find a clean, safe place from the abominations of the outside world, this is the experience he would potentially have, the «Father» thinks. However, it is important to understand that there are multiple reasons as to why he lies in the first place, one of those reasons, along with all the others are revealed later.

Sole Survivor: «It's really you... After all this time...»

«Father»: «Yes, it's true.»

«In the Vault, you had no concept of the passage of time. You were released from your pod, and went searching for the son you'd lost.»

Deliberately wasting Sole Survivor’s time constantly reminding him of something painful, he tactically tries to calm him down with the typical old man’s fairytales he had up his sleeve if the Sole Survivor would actually get to the facility. The longer he talks the calmer Sole Survivor would get and at some point, accepting. «Father» clearly uses the Sole Survivor’s lack of knowing how much time he had spent in the vault since the kidnapping. Interestingly enough, he knows the Sole Survivor’s story and is very focused on him since he first escaped the vault, which would only confirm he was the one behind the kidnapping mission in the first place, as that would simply not work if he was his real son, because if the kidnapping happened 60 years ago under a different Director which is not the case judging from Kellogg’s memory, he wouldn’t be told a thing, know his own «real» name and especially wouldn’t know where he came from for sure, not even who his parents were, as that was supposedly far too long ago. If he knew that the Sole Survivor was his parent, he would free him and especially wouldn’t do anything opposite to his safety throughout the game. «Father» is not ready to share any documentation with the Sole Survivor as there simply isn’t any, except for the one he put together himself 10 years ago.

«Father»: «But then you learned that your son was no longer an infant, but a 10 year old boy. You believed that ten years had passed. Is it really so hard to accept that it was not ten, but sixty years? That is the reality.»

It being 60 years since the kidnapping is a nonsensical lie, as the events are too inconsistent for that to be the case. How would the «Father» know that the Sole Survivor believed Shaun is 10 years old before he reached the Institute and why would he assume he was told anything about it? The answer being, «Father» carefully pre-planned his steps and sent Kellogg with Shaun into Diamond City, so that someone would tell the Sole Survivor they have seen a 10-year old boy, he uses Shaun as a decoy, which is confirmed in Kellogg’s memory. This is a well-thought out plan and now he lies to Sole Survivor that 60 years had passed. He lies to Sole Survivor in the most empty-worded and lame way possible. There are many points to make as to why it has been 10 years and not 60. First, there are a few things to look at intel-wise.

One of the departmental notices of the Institute that player can find if he does enough exploration gives him following intel that confirms most of the things «Father» tells him being a lie.

«Impending Arrival»:

«Father»: «Our monitoring of events on the surface has confirmed that the time is almost at hand. Very soon, our guest will be here. I admit that I feel both hope and trepidation when I think of how our first meeting will go.

Please make whatever preparations that you deem necessary. Consider all sensitive information to be classified for the time being. We cannot know for certain what our visitor's motivations will be, especially after coming into contact with the Railroad. We will exercise caution, but we must also extend a warm welcome. In time, once a measure of trust has been earned, we can be more forthcoming.

I need not remind you all how important this is to me personally, but I want you also to think of the opportunity for the entire Institute. We stand to gain a great deal if we make the most of that opportunity.»

A warm welcome is exactly what they’ve tried to achieve and trust from the Sole Survivor is gained through misinformation and deception. They know that the «guest» that is the Sole Survivor is nearly unstoppable, despite constant attempts at trying to execute him in different areas with the synths sent to catch him off guard, such instances happen many times throughout the game. Because they can’t physically defeat the Sole Survivor, they use psychological methods they have practiced for a long time for even greater achievement, making their worst enemy work for them. That is the opportunity for the Institute the «Father» doesn’t want to miss out on.

«Child synth prototype» intel:

«Father»: «I'm concerned at the pace of our progress in correcting the problems with the child synth prototype. I cannot impress upon this division enough the need to resolve these issues quickly and completely. Time and again, we've corrected flaws only to see them return. I find myself questioning whether we're thoroughly testing these fixes before moving on to the next item.

You know that I have great faith in all of you, but time is quickly running out. I must ask that you take whatever measures are necessary to meet the project targets within the time frame. Please make this your foremost priority.»

«Father» feels pressured as his time is quickly running out. That confirms synth Shaun being a new prototype developed very late for a malicious agenda and that the Institute made progress with the Gen-3 synths only fairly recently. He tricked Kellogg into thinking that it’s the real Shaun that got 10 years older behind his back and Sole Survivor about him being his real son. That decoy is an advantage to the Institute from both sides.

Intel of Justing Ayo, a Synth Retention Bureau director:

Director Ayo: «As you know, Father has granted full access to our new visitor from the surface. That includes the entirety of the SRB. While we must accommodate Father's wishes in this matter, we must also remain diligent.

Refrain from discussing any sensitive information, especially the ongoing investigation involving the gen 3 synths. In an ideal world, the Railroad will have had no influence on our new guest. We do not live in an ideal world.»

That confirms there is a sensitive and classified information Sole Survivor never hears.

Alignments regarding years and the events of the Fallout 4’s story serve as a hint, they are very fishy. The game takes place exactly 210 years after the Great War, 10 years after the events of Fallout 3 and synth Shaun seen in the game is meant to be also 10 years old. In the Institute there are personal logs of Brian Virgil he recorded before escaping the Institute, suggesting that the FEV experiments too lasted for 10 years.

Brian Virgil: «This will likely be my last recording. My requests to shut down the FEV program have repeatedly been denied. We've learned nothing useful in the last 10 years; why does Father insist on continuing it? If he won't see reason, then I have to take matters into my own hands. What we're doing... it's not right. It needs to stop. If anyone should find this after... after I'm gone... know that I never wanted to hurt anyone. Anyone! Do you understand me? I'm going to make sure the whole program is shut down. If not for good, then at least for years to come. After that...

...I know what I'm about to do will be seen as a betrayal. Treason, he'll probably call it. So... I'm leaving. I have a plan... and if it works, I'll be somewhere safe.»

Institute workers experimented on alive, kidnapped human beings which killed or turned most of the subjects into super mutants, these tests were possible most likely due to the Shaun’s DNA sample acquired 10 years ago, after that, they’ve immediately started it.

Kellogg, ridiculously enough is believed to be working as an Institute’s operator for over 60 years. No antagonistic mercenary like him would have patience or see the benefit to work for someone that long, especially with constant suspicions arising, he’d rather screw someone from the Institute over, find a way to gain benefit using his own ways or simply leave, him working for so long is unrealistic. «Father» tells him that the augmentations prolonged his life, though no one except «Father» himself ever references it to be the case, he was augmented specifically with the purpose of viewing his memories if they would suspect him of being a threat, that’s what the true function of his brain augmentation is. In the Institute player can find the personal logs of «Father», them being orchestrated wouldn’t be far-fetched, as he constantly contradicts his own actions in that terminal.

«Father’s» personal notes:

«The wait continues. Ayo can only confirm sightings outside Vault 111, and again in Diamond City sometime later. What that means, I'm not sure. Will we actually meet? Was this all for nothing?
No, not nothing. I will have learned valuable things about myself, my past, either way. I cannot afford to let emotion get in the way. I must simply observe and record.

I'm told Kellogg has gone offline. Strangely, I find myself thinking Dr. Walker. He had such high hopes for Kellogg. Such faith in the implants, and what they could mean. I still regret eliminating that project, but I know where it would have led us. Walker was never shy about his goals, and too many others were starting to listen. In the end, I believe I was justified. The Institute is about preserving humanity, not some bizarre amalgamation of biology and technology.»

Dr. Walker is the doctor responsible for augmenting Kellogg with the new experimental hardware. Their potential however was never truly solved, most likely they weren’t sure if they would work in the long run, it is said by «Father» that he has «regret eliminating that project». What’s also interesting is how contradictory statements of «Father» are. Later in the dialogue with the Sole Survivor, «Father» claims that he himself released him from the vault while in the terminal he’s talking about the «sightings» near the vault as if he’s surprised the Sole Survivor got thawed out «what that means, I’m not sure», he also sends Kellogg with synth Shaun to Diamond City, that was his plan, which is why Kellogg was suspicious of «Father». In the terminal he also acts as if he doesn’t know who killed Kellogg.

July 16, 2285

«Father»: «Kellogg's occasional presence continues to unnerve the others. At first, I thought they were merely intimidated by his confidence and arrogance. Or perhaps even afraid of his general being. Kellogg is, after all, a killer. But as I've continued to witness their reactions, gauge their sidelong glances, I've detected something else, something I probably should have anticipated - jealousy.

Kellogg is a living memorial to a forgotten program. He is an augmented human being, a cyborg really, and the benefits he has received cannot be denied. But really, the scientists here could not care less about enhanced reflexes or greater combat efficiency. No, the cause of their envy is something more practical, more primal - his enhanced life expectancy.

Just how long will Kellogg live if he passes naturally (however unlikely that may be)? It's hard to say. He's already more than one hundred years old. Older, certainly, than any other human in the Commonwealth. His complete physiology has been altered. Perhaps he'll make it to 150. Maybe even 200. Let the petty have their petty jealousies. Kellogg is a living testament to the ingenuity and superiority of the Institute. And I take no small pleasure in knowing that must irritate him to no end.»

It’s easily proven that the thoughts of «Father» written in his own terminal aren’t of his own, the terminal information is orchestrated. Judging from what «Father» tells Sole Survivor later in the dialogue, he’s only supposedly not very fond of Kellogg. The question is, why would «Father» write something spiteful about other Institute workers and commend Kellogg, the actions of whom, as Father says, he is not proud of in the dialogue with the Sole Survivor? Why would he write anything, especially that open in the first place? He comes up with the lies both in the terminal and in the dialogue, while the terminal information was intentionally prepared beforehand so that the Sole Survivor would be more confident in what «Father» tells him, except when Sole Survivor asks questions contradictory to «Father’s» actions when they actually met, he comes up with other contradictory lies hoping it would work. The reason of the terminal information being entirely different to the truth is because «Father» doesn’t suspect Sole Survivor viewed Kellogg’s memories that tell a whole different story. Institute, as «Father» says is keeping Kellogg «on a short leash», which means that they wouldn’t truly risk augmenting Kellogg prolonging his life for hundreds of years. Kellogg kidnapped Shaun 10 years ago and was rewarded with the augmentations, the true purpose of which was to view his memories, not for prolonging his life, this risk is something Institute wouldn’t afford. If they had advanced augmentations that prolong the life, «Father» himself wouldn’t decline such favors, they also would have a cure developed for «Father’s» disease that slowly kills him. Continuous failures at the FEV experiments, constant delays, setbacks, hardships with the Gen-3 synths for decades would only suggest they wouldn’t even have augmentations strong enough to prolong the life especially.

«Father»: «And here I am. Raised by the Institute, and now its leader.»

Sole Survivor: «But why? Why take a child? Why take you?»

«Father»: «Ah, now that's the question, isn't it? "Why me?".

Sole Survivor: «They stole you! Kidnapped you! It wasn't right!»

«Father»: «Right, wrong... irrelevant. It was necessary. The Institute believed humanity's future depended on it.

Sole Survivor: «It... It wasn't right, what they did. Taking you from me like that.»

«Father»: «To you, that would certainly seem true. But to the Institute... It made all the sense in the world.»

«At that time, the year 2227, the Institute had made great strides in synth production. But it was never enough. So they followed the best example thus far - the human being. Walking, talking, fully articulate... Capable of anything.»

Sole Survivor: «I think I see where this is going...»

«Father»: «Then perhaps you already understand why it was necessary for the Institute to acquire me. The Institute endeavored to create synthetic organics. The most logical starting point, of course, was human DNA. Plenty of that was available, of course, but it had all become corrupted. In this... wasteland... radiation affected everyone. Even in their attempts to shield themselves from the world above, members of the Institute had been exposed. Another source was necessary. But then the Institute found me, after discovering records from Vault 111. An infant, frozen in time, protected from the radiation-induced mutations that had crept into every other human cell in the Commonwealth. I was exactly what they needed. And so it was my DNA that became the basis of the synthetic organics used to create every human-like synth you see today.»

A child getting raised by the Institute, especially him becoming the Director is too far-fetched. Shaun was kidnapped for one specific reason and that reason only – for him to become a sample. Failures at the FEV research on alive human beings, constant deaths and troubled synth development process would only suggest one thing, nothing good would come off to the kidnapped child, Shaun would not survive the experiments, especially as an infant 60 years ago. Most of the synths being based on Shaun’s DNA is too, most likely, a lie, that simply wouldn’t work. First, irradiated DNA wouldn’t logically make the synth development harder, everyone in the Commonwealth is affected to radiation in any capacity, that doesn’t even affect their fertility. Second, synth malfunctions or hard Gen-3 synth development process is unlikely tied to DNA at all. In order to figure out as to why, there are more departmental notices from «Father».

«Father»: «As you are all aware, from time to time one of our Gen 3 synths assigned to surface duty will malfunction and go off assignment. While only a rare occurrence in the past, in recent months we have seen the number of losses rise noticeably.

Doctor Ayo has opened an investigation into this matter, and I must ask that you all give him your full cooperation as he looks into this troubling issue. Please answer his questions as completely as you can, and provide Dr. Ayo with any logs, materials or other items he requests.
With your help, I'm sure we can resolve this matter quickly.»

If the new Gen-3 synths are truly based on Shaun’s DNA, how come newer Gen-3 synths struggle of malfunction issues even more than ever before? If most of the missing subjects kidnapped by the Institute are M.I.A and are most likely dead, there is a high chance that the Institute needs more than just a DNA sample of whoever they kidnap in order to create an exact replica of one man, they likely undergo such complicated experiments that the original dies. Because Sole Survivor wouldn’t really know how this works, «Father» would know he is an easy target to lie to. Creating all Gen-3 synths based on Shaun’s DNA also wouldn’t make sense if they want to create an exact same version of a human they kidnap, DNA of each synth should be nearly an exact same, for personality traits too, to become exactly the same if they wish to replace someone in the Commonwealth for it to come off as an original. If it would be Shaun’s DNA that is used, all synths would be very different to a human they’re based off of and most importantly would have real Shaun’s traits, they however, do not, as each individual synth is based on DNA of a kidnapped subject, not on Shaun’s and creating a DNA from thin air, from scratch, to use Shaun’s DNA as a «base» is something completely unrealistic, impossible in any scenario, the truth is, you can’t even just «create» a DNA on a computer, it’s not how it works. There has to be a source of a DNA, but if it’s used for all synths, it would already be long gone, even then, they’d have to «clone» that DNA, except DNA’s of other subjects they kidnap are irradiated. Even if they would combine both the cloned Shaun’s DNA with the DNA of kidnapped humans to create a copy, the DNA of the end synth would too, be completely irradiated, as combining clean and irradiated DNA wouldn’t work. The only conclusion to make is that Gen-3 synths at the time of Fallout 4’s story aren’t based on Shaun’s DNA, never were, especially considering an ever larger amount of synths still malfunctioning. If the Institute wanted to create a synth, an exact copy of a human being, subjects would suffer extremely intense experiments that wouldn’t leave original human alive, which is exactly what happens with the people they kidnap.

At some point, even having an access to a clean DNA sample wasn’t enough, they couldn’t manage creating a synth with the same personality of a person they kidnap, while combining both DNA’s resulted and still, in many instances, results in the malfunctioning synths. There is a possibility that whether the synth is defective or not is not dependent on DNA, that explains as to why there were even more malfunctioning synths in the recent months, most likely, it answers that the creation of a stable synth is definitely much more complicated and isn’t just DNA based, which in favor, answers that Shaun wasn’t truly a base for the Gen-3 synths and that it’s once again an old man’s fairytale. Synth Shaun was created specifically for «Father’s» personal needs, which is why «Father» sounds very eager about an infant, protected from radiation, as if he’s the one who ordered a kidnapping.

It is worth noting that synth Shaun was created, with the key word being, «approximate», basically a rough estimation of how «Father» looked if he was 10 years old, so the synth Shaun you’re seeing might not be actually based on «Father» who is supposedly, as he lies to the Sole Survivor, is his son.

Taken from Madison’s Li notes:

Madison Li: «The official explanation for the "accident" in the FEV lab remains unsatisfactory. Facilities has nothing; they simply refer me to the Director. And he's keeping something from me. I've been around long enough to see it.

I wonder if he ever considers the ramifications of what he's asked me to do? If he worries that having me build a synth that's supposed to approximate him as a child might give me some unintended insights into his character? Probably not. And to be honest, it probably won't.»

It is important to remember that Madison Li came to the Institute just recently, she wasn’t working for the Institute at the time of Fallout 3 in the Capital Wasteland, which means that she wouldn’t know of all the Institute’s secrets and especially the original look of «Father». In order to come off as the Sole Survivor’s son, he goes through a surgical operation that would roughly resemble Shaun while the synth Shaun is built off of a real Shaun’s DNA, though reconstructed specifically to how «Father» looks. That is supported by a very limited change in facial features of «Father» in the game itself, as mostly only the skin color changes, there is no complexity that would make him look anywhere close to Nate or Nora, the same with the synth Shaun, so regardless of how Sole Survivor’s face looks, «Father» wouldn’t really look like his supposed parents. Synth Shaun is based on real Shaun’s DNA, not on «Father’s». Personalities of synth Shaun and «Father» are very different. If Sole Survivor destroys the Institute and takes synth Shaun with him, he would know more about the synth Shaun’s personality. «Father» hates Commonwealth and thinks there is no way to save it, atleast that’s what he tells Sole Survivor to get him to his side. If «Father» steps to the surface he references the state of the Commonwealth:

«Father»: «This just confirms the truth I've always known. The Commonwealth is... dead. There's no future here. Standing here, I'm reminded of how fortunate I am that I was spared a life in this wasteland.»

Contrary to «Father», synth Shaun is impressed by the Commonwealth and opposed to him, considers Commonwealth a hopeful place.

Synth Shaun: «Doctor Watson always said the surface was hopeless. But it's not! Just look at what people are building! People out here are just like me. They like to tinker with things, too! It can be scary out here sometimes, but people just never give up, do they? They're always trying to make things safer.»

«Father», as soon as he steps into the room to welcome the Sole Survivor talks about how the child’s responses are not the ones he anticipated. The reason being, synth Shaun’s DNA basis being that of a real Shaun. That is also confirmed by the sudden, unclear memories of him being an infant:

Synth Shaun: «Did you know me when I was younger? I... I can't remember.»

If the Sole Survivor asks synth Shaun about the «Father», he’ll tell him that he doesn’t tend to visit him too often. That is the result of synth Shaun serving as nothing more but a caged sculpt the «Father» admires, there’s also a much more uncomfortable reason as to why he keeps him in the first place that is revealed later if the parallel is drawn.

Synth Shaun: «Father? He doesn't come visit very often these days. And even when he does, he usually just talks to the other doctors.»

«Father says I'm "fascinating." That's a good thing, right?»

«Father» doesn’t share any views or has any personality connections to the synth Shaun, because synth Shaun was only sculpted to look «approximately» like «Father», but the DNA is based on the real Shaun. That makes «Father» even more antagonistic that it seems.

Coming back to the dialogue between the Sole Survivor and the «Father»:

«Father»: «I wish there were something to say. I know this isn't what you wanted. But it's the only truth I can offer you.»

That is the only «truth» he can offer him as the real one would instantly make the Sole Survivor turn on «Father» and he would become hostile. It’s critical to him to hide the real information about his son being dead.

Sole Survivor: «It can't be true. It's all just... It's just too much.»

«Father»: «I've shown you my trust. Your weapons haven't been confiscated, and I stand unarmed before you. Please, let's just talk.»

Yet again, a lie. «Father» actually is armed and carries an Automatic Institute pistol and some fusion cells with him.

Sole Survivor: «Why are you doing this to me? After everything I've been through...»

«Father»: «I don't mean any of this to hurt you. I'm just... I'm trying to help you. Help us.»

«Father» tries to convince the main character with the only «truth» he’d want to hear so that he’d help them and be a part of the Institute. A very malicious last sentence shows that. He wants Sole Survivor to side with him against all other factions of the Commonwealth, since they are extra pressured by the BoS arrival.

Sole Survivor: «You're lying. I know it.»

«Father»: «Why would I lie? What would I have to gain from it? I assure you, this is the truth.»

He’d gain a few things from lying to Sole Survivor.

1. Sole Survivor would stop looking for Shaun, he’d put his search to rest and believe in old man’s fairytales.

2. Due to him finally «finding» his son he would hesitate at killing «Father» and blowing up the Institute.

3. He would become the Institute’s director, the strongest and most resilient man of the Commonwealth would believe in questionable Institute’s ideologies and take a role of the Director when «Father» dies of a progressive disease. «Father» has nothing to lose by his warm welcome, so if the Sole Survivor would turn on him, he wouldn’t care too much, as he is dying either way. Even if Sole Survivor would leave the Institute, he would still believe that «Father» is his son and would think twice about blowing up the Institute and siding with any other faction.

4. «Father», due to his progressive disease wants to die around the «family» he loves. Even if he created that family all by himself. For a long time «Father» had no love to feel, this is exactly what he states later in the dialogue, this is also, partially a reason as to why he wants Sole Survivor to think that he is his son, he wants to be taken care of and feel love, as if synth Shaun is «Father’s» son and Sole Survivor is his real father. Synth Shaun was created for his own «creepy» reasons, for the same reasons he lies to Sole Survivor about being his son.

Sole Survivor: «Kellogg… He worked for you?»

«Father»: «Kellogg... He was an Institute asset long before I arrived here. It wasn't until I became
Director that I learned of all the things he'd done... what kind of man he was.»

At that point Sole Survivor asks a very sensitive question that is difficult for «Father» to answer, he tried to avoid that question at all costs. Him lying to Sole Survivor and imagining the most fitting answer is obvious as right after he references Kellogg, he looks to the right, changes his tone of voice to a more irritated one and takes time to come up with the answer. In fact, he is fond of Kellogg's cruelty, he smiles when talks about «what kind of man he was» though, he still prefers keeping him on a leash because he, eventually, lost his trust. Sole Survivor catched «Father» off guard by asking that question, evident by him getting surprised and irritated by an inconsistency he forgot and didn't want to bring up.

Sole Survivor: «You knew the man was a psychopath, but you used him anyway?»

«Father»: «Would have preferred that I turned him loose on the Commonwealth? At least keeping him on a short leash kept the collateral damage to a minimum.»

«Father» is not very trusting of Kellogg, that’s why he never briefed Kellogg on anything more than «need to know basis». The Institute also wouldn’t realistically augment Kellogg they’re trying to «keep on a short leash» with the augmentations prolonging his life. That wouldn’t make any sense, so «Father» is coming up with that lie later in the dialogue contradicting his earlier statements and even actions. He was augmented so that the Institute would have an access to his memories, just in case and it was 10 years ago.

Sole Survivor: «He was a murderer. He killed your mother.»

«Father»: «Believe me, I am well aware of the atrocities Kellogg committed. I suspect there are many more we'll never know of.»

«Father» knows something Sole Survivor doesn’t know. In his voice lines he doesn’t show any care at all when the parent is referenced, he’s angry at something else. In reality he is angry that Kellogg pretty much refused to go to Glowing Sea and instead hid in his base of operations, as he suspected he is being set up. Kellogg failed to eliminate Sole Survivor and that way put the whole operation in danger, also directed him to go find the Institute, as he himself suspected that Shaun is 10 years old and that he naturally grew over time since he first kidnapped him 10 years ago, that’s why Kellogg was so confident that Shaun is «with the people pulling the strings».

«Father»: «But yes, I understand you've... experienced things. Perhaps you ended up knowing him better. I, for one, will never truly forgive him.»

He is worried about the «collateral damage» Kellogg committed by killing Sole Survivor’s spouse, but it is important to not confuse that he feels that way only because he didn’t obey his orders of leaving two backups alive instead of just one before he kidnapped Shaun, he doesn’t feel any emotions towards the feelings of Sole Survivor or spouse’s death, as none of them are his real parents anyway.

«Father»: «My parents were supposed to be kept in cryogenic suspension should a, uhh, "backup" be required. But none was necessary. The program was ultimately a success; my DNA was fused with a modified virus to create the organic material from which our new synths are made.»

Judging from how many failures there are regarding FEV research, it is unlikely any of that was a success and, due to even more malfunctions in the recent months, wasn’t.

«Father»: «The Institute took advantage of Kellogg's vicious nature. I will freely admit that.»

Even though «Father» is mad at Kellogg for continuously disobeying orders, he is glad that he killed his spouse at the very end. That way he’d deal only with one man instead of two.

«Father»: «Institute technology prolonged his life, and his usefulness, far beyond any normal human life span. He never failed the Institute, but his cruelty became more apparent with every completed objective. I won't lie: it's no coincidence your path crossed his. It seemed a fitting way to allow you... us... to have some amount of revenge. What else can I say to ease your mind?»

It’s very clear that he comes up with lies in progress with constant stutters and uncertainties at what to say, specifically, as he says, to ease Sole Survivor’s mind. He pretends that they’ve met the common goal, which is not the case, unless Sole Survivor believes in his lies, that is, also admitting that he did use synth Shaun as a decoy so that Sole Survivor would know of his whereabouts.

When asked about the spouse, he says the following:

«Father»: «Yes, what happened to her was... I've gone over the records of the incident, of course. It seems her death was an unfortunate bit of collateral damage.»

Sole Survivor: «"Collateral Damage?" Is that all it is to you?»

«Father»: «I forget that it's been such a short time for you. I don't have any direct memories, and I've had my entire life to cope with the loss.»

When asked, this time he tries to be more forthcoming, but lies about having any emotion regarding that subject, as he was the one responsible ordering Kellogg to retrieve a kid and was the one who marked spouse’s death as «collateral damage», as they’ve wanted to use their DNA if Institute failed to retrieve Shaun’s samples. It is very obvious by his body language and time it takes for him to come up with an answer that he lies, he also forgets that he lied to Sole Survivor about finding out who his parents were only when he became a Director and instead says he had an «entire life to cope with the loss.».

Sole Survivor: «She was murdered!»

«Father»: «Killed, yes. Murdered? I'm not so sure about that. Still... I do regret never having known her.»

He subtly tells Sole Survivor that there would have been much more collateral damage if she wouldn’t have died, he thinks she was killed and not murdered as if her death only helped the Institute.

Sole Survivor: «Shaun, she loved you... so much.»

«Father»: «I have no doubt. I'm afraid I have little experience with those emotions, having lived my life within the Institute.

Sole Survivor: «So you're in charge of the Institute?»

«Father»: «I am the acting Director, yes. I spent decades working to reach this point. It's a responsibility I take very seriously. The Institute... It's important. It really is humanity's best hope for the future, no matter what those above ground might think of us.»

Once again empty words and an attempt to brainwash Sole Survivor. Everything that the Institute did resulted in failure and harm, replacing humanity with synths couldn’t be a humanity’s best hope.

Sole Survivor: «But... Director? Why you?»

«Father:» «I was the most qualified for the position, obviously. I've lived my life within these walls, dedicating to science like every other member of the Institute. My hard work has paid off. Ultimately the Commonwealth has nothing to fear from us. Whatever you've seen or heard, I know I can convince you of that. Just... give me time.»

Even if Shaun would work years at the Institute, the competition with so many workers would be tough and it’s unlikely that if Shaun did survive, he would be put in place as a Director, that sounds like a bed time story if anything, real Shaun would know what happened earlier and would have large suspicions that he was kidnapped, he wouldn’t like what the Institute did.

Sole Survivor: «They need your help, Shaun. It's rough up there, to say the least.»

«Father»: «Oh, we've tried that. Surprised? The Institute once tried to help create a stabilized Commonwealth government. It ended in bickering, infighting... it was a disaster. No, we look after our own now.»

Institute did not try to create a stabilized Commonwealth government, instead, it tried to prevent it from occurring during CPG Massacre, that’s the reason of why synth was sent to the meeting murdering everyone.

«Father»: «I know there's more for us to discuss, but... The Institute is on the verge of some important breakthroughs. Your presence would be... appreciated as we approach them.»

Yet again, unlikely that only 60 years from Shaun’s kidnapping they would be on the verge of important breakthroughs only now. Starting from Shaun’s kidnapping, more recently synths malfunctioned in greater amounts than ever before.

«Father»: «I've been a part of something amazing here. I've helped to build a life for myself and the people of the Institute... and now, after all these years, you have an opportunity to help with that. Doesn't that intrigue you? Isn't that what you want?»

«Father» gets more and more desperate as the time is running short, he doesn’t know what to come up with and tries his best to lure him in.

«Father»: «I hope you can see that, rationally, the Institute is the only thing left in the world that's worth being part of.»

Sole Survivor: «How can you say that? How can you be so dismissive of all those people, everything they've done?»

«Father»: «Because it is the simple truth, and I believe you know it too. I simply ask that you give the Institute.... me... a chance. A chance to show you what I've been telling you.»

Coming back to what Deacon said, it works as a distinct parallel:

Deacon: «We've come a long way since the beginning. We've done a lot of good. Saved a lot of synths. But we're about more than that. We're the last and only line of defense between the Institute and the Commonwealth, maybe even the world.»

Sole Survivor: «You've lied to me at least once. This is just more of the same.»

Deacon: «Yeah, you got me. But you're going to hear the same sort of lies elsewhere.»

«Father»: «For now, it's enough that you understand that the Institute really is devoted to the betterment of humanity.

If that trick did not work on the Sole Survivor, «Father» is disappointed:

Sole Survivor: «I can't afford to trust anyone.»

«Father»: «I see. I am... disappointed.

Sole Survivor: «Your Institute has done some horrible things»

«Father»: «What about the people you've aided in order to get here? What atrocities have they committed? These Minutemen, claiming to want to save the Commonwealth... from itself? They cannot even protect themselves. Their cause is a doomed one. None have any true claim to nobility in this world. Those days are gone. But we are not the monsters we have been cast as.»

Minutemen is the only faction in Fallout 4 that tries to help the humanity in any way they could, putting their necks on the line. As simple and as ironic as it’s done in the story, Minutemen is the only faction that can save the humanity through constant Preston’s radiant quests that the Sole Survivor would do for the whole eternity, saving Commonwealth time and time again. Not far-fetched that they infact can save the Commonwealth.

If Sole Survivor denies «Father’s» request:

«Father»: «I had certainly hoped we could work together, but every man must make his own decisions. If you choose to leave, I cannot force you to stay. Understand, though, that I cannot allow you to remain within the Institute.»

At that point their warm welcome theater would be over and «Father» does everything he can to show the Sole Survivor he’s not his son, all he wanted is to deceptively program him against the Commonwealth.

«Father»: «You may have safe passage back to the Relay where you will be sent back to the surface, but from that point... you must be considered hostile.»

If asked by Sole Survivor what is the purpose of creating a child synth he would avoid the question at all costs, saying that it’s just an «interesting variation». From that point, however, if player decides to side with the Institute he performs and experiment on Sole Survivor, interested to see if he would still love synth Shaun despite him not being the real one.

«Father»: «But... I'll admit, I'm curious. As a parent looking for his child, looking for the younger version of me... What do you think? Do you think you could love him? Like you would a real boy?»

His most important replica during the whole dialogue, if player without any questions believes «Father's» lies, he would "break a fourth wall", by staring into the camera, look away and for an entire second evilishly smile before an instant facial expression transition:

«Father»: «Forgive me. I'd assumed that after everything I'm sure you've seen above ground, you would be... more than a bit biased against us.»

«Father»: «You know, in all my years, I've never set foot outside the Institute. Not once, since the day they brought me here. I've never had a reason. But now... this just confirms the truth I've always known. The Commonwealth is... dead. There's no future here. The only hope for humanity lies below.»

At that point, «Father» pretends he doesn’t know what the Commonwealth looks like. He is aware of everything that happened, even what factions are present in the Commonwealth with their specific ideologies. That way he tries to make Sole Survivor give up on Commonwealth and when he becomes the Director, after «Father’s» death due to a disease, Sole Survivor would continue his legacy of doing evil from the shadow. If they had humanity’s best interest he wouldn’t state the opposite after that.

Sole Survivor: «So why come out here?»

«Father»: «To put things in perspective, I suppose.»

Sole Survivor: «They left me on ice... for sixty years...»

«Father»: «They did, and for good reason.»

Sole Survivor: «Kellogg called me the "backup."»

«Father»: «Did he? Well, he was correct.»

«Father» pauses himself after that question, now a «backup» acquired a whole new meaning, as he did not expect lies to work so easily on Sole Survivor.

«Father»: «I'll admit, when I had you released from Vault 111, I had no expectations that you'd survive out here, in all this. To not only do so, but manage to find me... to infiltrate the Institute itself... Extraordinary.»

Sole Survivor: «You could've let me out decades ago!»

«Father»: «Until I became director, I had no idea you were there. And after, there was initially no... logical reason to do so. Certainly it was no longer necessary to keep you suspended... I... Well, I suppose I wanted to see what would happen.»

If asked as to why he let him out he stutters and can’t come up with anything else:

Sole Survivor: «Why let me out now, after all this time?»

«Father»: «That's... well, that's hard to explain.»

Sole Survivor: «So it was you. You let me out.»

«Father»: «Yes, it was my decision. An experiment, of sorts. I had no idea what kind of man you were, you see.»

«Father» is not the one to place bets, releasing someone who’d cause more harm to the Institute is something he wouldn’t risk, especially with the spouse killed by the Institute affiliated mercenary.

The truth is, everything «Father» said, including that he is his son is a complete lie from the beginning to the end. He did not refreeze the Sole Survivor, nor it was his decision. What happened exactly is not a mystery.

Vault, at which the Sole Survivor was frozen in was also an experiment, just like all the other vaults. Each vault in the Fallout universe is created as an experiment, to test the results of different outcomes. In that vault, cryogenic suspension was tested to see if a human being can survive being frozen for a long time, but because cryogenic pods were never tested before, nobody knew what you can expect from that. Cryogenic pods had a tendency to malfunction if a human is kept frozen for long enough, the cryogenic array at some point will start thawing the subject out.

System malfunction terminal:

«Strange issue today with pod C3. Subject appeared to be having heart palpations. Nothing life-threatening, but unusual. We realized almost too late that the pod was malfunctioning. The cryogenic array almost started thawing her out.

We're not sure, but I suspect a hiccup in Vault-Tec's remote override systems may have sent an errant signal. We'll have to keep an eye out. I only hope their systems are reliable once we evacuate the staff.»

Kellogg himself doesn’t know how did Sole Survivor manage to get thawed out, the Institute never wanted him to. Sole Survivor was kept as a potential DNA backup, but even if he would get thawed out, Kellogg thought he could defeat him, as he stated before. They left Sole Survivor in cryogenic pod and completely forgot about him, as even the «Father» himself didn’t expect him to survive the Wasteland and when the situation got tighter, the Institute kept sending synths to silence Sole Survivor, synths that follow him throughout the whole game and are attempting to catch him off guard coming in through the entrances of the interiors he visits, sneaking from behind. At last, if player attempts to open cryopods, the terminal gives out an error - "Malfunction in cryo pod manual release override" which suggests that no one would be able to release Sole Survivor manually, while the «Father’s» terminal suggests he was confused about sightings near the vault, contradicting him stating that he was the one who decided to release him.

«Father»: «I can accept that you're offended. You must understand, though... I have had no love to feel. We have been strangers until now, you and I.»

...

Kellogg: «I never knew why we didn't just refreeze the rest of them, but we had our orders. I guess the old man didn't want so many loose ends. Too bad he left alive the one person he shouldn't have.»

«Father», the main Institute’s Director is diagnosed with the progressive disease right before the Shaun's kidnapping, 10 years before the events of the game. To achieve his dreams, he gets hungry for a clean source of a DNA, sends Kellogg to retrieve Shaun. Due to the DNA backup, Sole Survivor’s spouse getting killed, it leaves him and Shaun being last backups. Life support for all other cryopods was cut because there were too many witnesses, them being «loose ends» that would be dangerous to let out. When Shaun is delivered to the Institute, «Father» gets mad at Kellogg because of the «collateral damage» he committed, and disguises the new augmentations as a reward, but in reality it was done so that the «Father» would be able to observe Kellogg’s actions, as in his eyes, he lost his trust because of what happened at the vault. He wanted more control over what Kellogg was doing. Shaun was then used for the «child synth project» that would serve «Father’s» loving interest, as he always wanted to have a son with clean DNA and would want his son to be young at all times as a synth, they don’t age. He sealed him off in a cell so that he would not get exposed to radiation if it was to come in with the Sole Survivor, he, however, loves him as a sculpt with no real emotional love towards Shaun. Shaun wasn’t used to create Gen-3 synths, he was taken specifically for the «Father’s» fantasies and the Sole Survivor, his spouse were supposed to serve as a backup of a clean DNA if the project would be a failure. It, however, wasn’t a failure, «Father’s» life slowly kept reaching it’s end, as to why he rushed synth Shaun’s development and has set a time frame. Changing his face, or skin color just in case if he would have to come off as Sole Survivor’s son, roughly estimating on how the Sole Survivor looks like, but not exactly, hiding the information from Madison Li, he hired her to use Shaun’s DNA and create him a 10-year old boy that looks almost like «Father» because he wants to fantasize him being his son. He didn’t much care about his looks anymore, as he was dying. «Father» knew that it takes much more than just DNA to create synths, they never achieved creating synths that wouldn’t malfunction and go off assignment, Shaun’s DNA could have been used in a parallel for the FEV research, but even that was a failure. It wasn’t the main true reason as to why he was kidnapped. Creating child synths is proven to be a much harder and slower process than creating an ordinary synth. Because "Father" never had a son and even a loving father, it was his dream to have a loving family before he passes away and in his case, it wouldn't be too extreme for him to create one, hence his love for what is synthetic rather than real.

«Father»: «With old age comes regret, and asking "what if..." more often.»

Sole Survivor gets thawed out 10 years later due to the pod malfunction and looks for his son. «Father» has gotten reports about the «sightings» near the vault and sends synths to eliminate him, he wouldn’t want to risk all the Institute’s research and wouldn’t want him to know the truth of what happened to his son. That was a failure and Sole Survivor turned out to be much stronger than first anticipated. «Father» sends Kellogg and synth Shaun to Diamond City, using synth Shaun as a decoy so that Sole Survivor would get information as to where the Kellogg lives by other residents and eventually, would have to face Kellogg in a fight. Kellogg wasn’t set up, as the «Father» wouldn’t want him to get him killed, he was only used as an asset that would kill Sole Survivor. «Father», however, «started losing his grip» and was forced to send Kellogg to Glowing Sea to kill Virgil, as he is the only one who can help Sole Survivor get to the Institute, it is a critical assignment he has given him and the «Father» wasn’t confident the decoy that is synth Shaun would work. He would rather prevent all possibilities of Sole Survivor getting to the Institute rather than hoping for something that is unlikely to happen. After that, Kellogg doesn’t obey «Father’s» orders and hides in his base of operations with old synth gen models programmed to assist him instead of going to Glowing Sea. Sole Survivor eventually follows him by his footsteps, gets information that his son is «with the people pulling the strings», kills him and retrieves a brain augmenter, later used in the Memory Den connected to Nick Valentine to view Kellogg’s memories. It wasn’t just the brain plugged in into Nick Valentine, it was the device recording Kellogg’s memories specifically. Knowing of the information as to where the Virgil is, he heads to Glowing Sea. «Father» in parallel writes a script on what to do if he was to get to the Institute, orchestrates his own terminal information to later contradict it when he can’t come up with anything else. After getting involved with factions of the Commonwealth, with Virgil, he finally reaches the Institute. Sole Survivor is getting psychologically tampered with, as now, at the last line of defense, this is the only weapon they can use. Institute’s Director is closing in on his death, has nothing to lose, fear and pretends to be Sole Survivor’s son. Before he dies, he would want to feel himself in a family, he is delusional enough to not just lie, but make himself believe the Sole Survivor is his true father to gain pleasure at doing the last terrible thing in his life before he passes away, that’s how evil he truly is. Brainwashed Sole Survivor, the Institute’s strongest enemy would now be it’s leader, continuing the legacy of «Father» at destroying the human race thinking he truly was his son. That way, every alive organism in the world, at some point, would be replaced with synths. If Sole Survivor refuses to side with the Institute, he is instantly considered hostile by the «Father» himself and is sent on his way back to the surface. The Institute, will then, have to get blown up.

Whether deliberate or not, the story’s stupidity, if you will, created whole new layers of meaning.

«Father’s» lies are very deliberate and specific. The whole game leads up the player to the one big lie, notably, inconsistencies of which aren’t clear to an extent that no one would even guess of the intricacies done by the developers with the lies done to the player throughout the whole game. What is also important to state is that the community is, truly, unwilling to pay attention to the stories, do research and would instead believe everything written on the fandom wikis, the ones that strangely enough, nearly always exclude the possibility of «lies» present within the game’s narrative. If the character states something with no evidence, just because he sounds sincere, it is widely accepted that this is the truth, simply, because it is said by a videogame character. It is always important to pay attention to the story, connect dots together and resolve any inconsistencies, which relates to the writers, as well as community. There’s always information to be extracted and there are always parallels to be made with real life and what you’re being told, instead of blindly believing one’s words even if the whole of humanity believes in one lie they spread like a virus. Do the research others wouldn’t do…