Walkthrough that includes Learn Everything About Everything (You opened all the logs of the Nautilus). They are marked with the bullets below.

For the record, you can press and hold right arrow to speed cycle through the logs.

If you don’t need that achievement you can technically ignore the logs except the one in the Garden is needed to get the piano keys to progress the game.

When you start you will leave your ship to the Nautilus and encounter your first terminal.
Enter your name or whatever you want to be called.

: First Contact (You encountered Kaizen-85).

• Show logs on terminal in the airlock after leaving your ship.

Open D2 to enter the Lobby.

• Show logs on terminal in the lobby (second room) with the TV playing.

Open D3.

Enter corridor. In this circular corridor there are 4 terminals.

• Show logs on terminal outside D3 Lobby door. Gives memory address: 0x008DA1DC
  
  
• Show logs on terminal outside D4 Living Room. Gives memory address: 0x0089AA2A

Open D4

: I'll Be Back (You waited before entering the living room). Just wait for Kaizen to say its okay to enter. You will hear piano music.

• Show logs on terminal inside D4, above Piano.

Leave.

• Show logs on terminal outside D5 Nandi’s bedroom.

Open D5.

Discover you need to trick the retina scan. Sticky note on terminal mentions profiler.sh and one on the floor has memory address: 0x0000884E which opens the eye image. When it asks for a retina match type A E N L. Then goto the scanner on the right side of door.

• Show logs on terminal inside D5.

Inside D5 Nandi’s room. Use the terminal, type to Open Bathroom, walk inside. Ask terminal to lift bed, walk under and go back to the terminal. During one of the interactions with Kaizen is when the explosion triggers. Wait for it to throw you out the window.

: A Wrong Place At A Wrong Time (You survived the accident in the bedroom).

Hold right mouse to stabilize .
Left mouse to thrust forward.
Thrust to the airlock D10.
Marked with this transistor symbol, kinda looks like a nano USB to me or a jellyfish :D:

Talk to Kaizen on the terminal. Depending how your interactions have been with him he may let you right in, or he may quiz you cause he thinks you are dead. If you were mean, he likely will toy with you which yields the 'Im afraid I can't do that achievement'.

Enter D10.

• Show logs on terminal inside D10 airlock.
  
• Show logs on terminal inside D11 Garden. Gives the piano hint B2 E3 F3

Type ‘elevator down’.

• Show logs on terminal inside the elevator.

Type ‘elevator up’ to go upstairs.

Straight across enter D4 Living Room, to your right is the terminal.
Type 'play piano', pick Manual and enter Q R T which is what B2 E3 F3 translated to.

: A Haunting Tune (You found a very singular use for the piano).

Play the mini game. You have 24 moves to cover the grid. The 25th it will overload and restart. Pressing the green character with the most on screen is advised.
Afterwards wait to see the message you enabled antennas and can control the Helix probes to get Anele’s room coordinates, HT34DF.

Elevator down.

On the garden terminal open D11.
Then open D10 to open the airlock into space.
If you cannot open the door you may need to engage in some dialogue with Kaizen. Possibly to apologize, finish the conversation with your plan with the helix probes, possible to mention more about Anele/Nandi, or to convince Kaizen you will return if he lets you out of the airlock.


There is 3 antennas. One below the ship, one above the ship and one off to the side wing.

When you get close a terminal will flip down (there are no logs here). You need for each green letter to come across the center darker grey line and press H T 3 4 D F as they do to match the corresponding character. If you accidently press something and stop a line on the wrong character just press that character that is on the darker grey line and it will start moving again. Remember right click will stabilize you in front of the terminals.

Afterwards thrust to the center middle where the probes went and into the broken window.

• Show logs on terminal in this room, Anele’s bedroom.

Ask Kaizen to open bathroom. Float into the open ceiling tile to find the Dairy floating there to get your code for D7 Bridge. In all my playthroughs its always been here, but people in the discussions have said they found it floating above the bed too.

: Dear Diary (You found the bridge password).

Thrust back to the D10 airlock.

Open D11, Elevator up, and walk over to D7 again.

• Show logs on terminal outside D7 Bridge.

I got : Shall We Play a Game? (You did small talk with Kaizen). In the terminal by D7 before entering the diary code; I typed, “How are you doing Kaizen” and this triggered. Prior to this I was just trying to be polite and engage in friendly banter. Basically, do more than the basic commands as I was going for the Delivered on a Promise achievement too which requires being super nice it seemed like.

Move on to enter the code you just recovered. This has changed on every play through.

Walk through the many doors going down this long corridor.

• Show logs on terminal inside Bridge.

: Learn Everything About Everything.



Depending how you treated Kaizen and your responses in the bridge you will get 1 of 3 endings:
- Together, Forever
- The Nautilus Is Yours
- Delivered on a Promise

• (You reached the “Together, Forever” ending).
  
  Blew up the drive with memory address 0x4A8511ED & said yes to merge with Anala and followed her to the exit.
  
  Additional input from others:
  
  Chromeo:
  BTW you don't have to destroy the drive to get "Together, Forever", if you tell Kaizen you refuse to destroy it you'll get Anele's interface window pop up. Seems like a better ending since it will take 30 minutes to get back to Earth instead of who knows how many centuries :P
  
  
  

• (You reached the "The Nautilus Is Yours" ending).
  
  Restored my first checkpoint where I got Together, Forever. Asked Kaizen to take me to Earth, take me home, go home… until he gave up control cause he was sick of me.
  
  
  

• (You reached the “Delivered on a Promise” ending).
  
  I was SUPER nice to Kaizen the entire run. Said thank you and please and used friend and buddy every chance I got. Used extra dialog just being nice like he was my friend.
  
  After Anala made her presence, asked, “Kaizen are you okay?”, “Im glad you are okay friend”, “can we go home now”, at which point he said yes and then I closed with “thank you friend”. To which Kaizen replied, “I must admit that your politeness itself deserves this trip back to Earth. I have counted at least 18 ‘thank you’ since you arrived 😉” One more “can we go” and his end dialogue to apologize and clear his conscience and then I replied that I forgave him and onto Earth we went!
  
  Additional input from others:
  
  AC-130H "Spectre"
  I was a total ♥♥♥♥ to Kaizen and I was near to death in front of the airlock as well. I said sorry, he let me in and then I used thank you and please, that was enough to get the perfect ending "Delivered on a promise" ;)
  
  The Metric System
  I got "Delivered on a promise" by using the profiler on the bridge to blow up the drive, talking to Anele, but outright refusing to help her (it takes 2-3 direct refusals to her) then Kaizen came back and took me to Earth with the emergency engines. I was polite to Kaizen but not super-polite.[/list'

I was a total a-hole to Kaizen. I kept calling him names, a liar, saying I didn’t care, being a general turd. After getting the diary code on the terminal in that room I ticked him off enough that he threatened saying I didn’t want to make him angry and I called him a few more names and comments.

At the terminal to open the airlock inside he laughed at me as a warning noise was going off that I was about to run out of air.
Me, “im sorry open the door”.
Kaizen, “You don’t look so good. Is everything okay?”
Me, “im going to die”.
Kaizen, “Okay, listen to me very carefully: that was the last time you talked to me like that.”
Me, “im sorry”.
Kaizen, “I will only let you in if I can trust

Enter profiler.sh on a computer and enter the following:

0x008DA1DC Show logs on terminal outside D3 Lobby.
0x0089AA2A Show logs on terminal outside D4 Living Room.
0x003DD427 Scarecrow & LastHopeFate mentioned it is triggered on the Garden console.
0x00A8079F Scarecrow mentioned it is triggered in Anele’s room.
0x00303F83 cyanic said you need to ask more questions about United Earth.

I got the Garden purely by accident my first play through but have not been able to trigger the last two myself. Thanks to those who were able to find it and share it.


Additional input from others:

Laza
A few notes about getting Things are Things:

1. You can get all five codes in a single run.
   
2. The code in Anele's room is triggered by repeatedly bringing back the comversation on Anele, but before retrieving the diary. (For more time with Kaizen, activate the antennas, go back to airlock to resupply the oxygen and only then go to Anele's room.) It might also have something to do with activating first either the bed or the bathroom (in my case, it was the former).
   
3. The code in the Garden is triggered by talking about memory accesses and memory clusters.
   
4. You can PROBABLY get both codes from a single terminal, either in Anele's room or in the Garden (though I haven't been able to do so and I don't know if it's doable in the same run).
   
5. The achievement pops up as soon as you read the last code on profiler.sh.