There doesn't seem to be any walkthrough apart from the achievement guide so I ended up making one.

I'm not sure whether a second playthrough is needed or not to get 100% achievements, but since you need to load a certain chapter (chapter 3) after you get the true ending, I assumed that you need to restart that chapter after reaching the true ending (not reloading a save that was done before reaching the ending). If you know more, feel free to let me know. As for other endings, I tried to make them obtainable in a single playthrough.

Follow the tutorial until the traffic light ask you to touch a blue shoe. Touch the blue shoe, and then touch everything in this area to see where the crow is. It'll lead you to the east exit.

Shake the fence nearby and pick up the Red Marble.
Red marble
Find the red marble


Head all the way to the east until you see the crow. Give the marble to it to get the Key.
A key
Find the key.


Touch the door on the top right corner to see Miss Sakura going to the bottom right corner. Use the key to that door.
Encounter
Complete #0.

Head all the way to the east, interacting with everything if necessary.
Thinking
You can now collect your thoughts.


Touch the flower pot after the cutscene. The exit is on the far east from the flower pot. Use the elevator.

Talk to the hotel manager and ask about Miss Sakura. Ask him to read the book in your inventory. Use the elevator to go to the cafeteria and touch the table.
Talking
You can remember the conversations you had.


Notice an aquarium that is newly placed on the area. Interact with it, ask about Miss Sakura, and ask about the book in your inventory. Use the elevator to head upstairs and head to the west exit.

Interact with the sleeping penguin. Shake the pole next to it twice to drop the sign, waking it up. Talk to it and ask about The Mirage Library, and then go to the hotel manager to ask about the engineer. Head to the employee area.

You can't use the elevator right now, so head inside the building to the west. Open and touch the right locker to see the lever that you need to pull (right lever). Pull the lever. Return to the elevator and use it to go down.

Interact with the mop (the game won't give you pointers for this) and touch it.

Return to the place with switches.
Touching
You can remember the things you touched.


Find a cap hanging next to the switches.

Shake the cap to reveal a lever. Pull the lever.

Check the mop's memory (you can check it from the menu) to see the lever that you need to pull between the 3 levers (pull the right lever up, pull the middle lever down). This will unlock the elevator to the top floor. Use the elevator.

Read the memory of the desk lamp and touch the TV on the east (you need to discover it).


The scene will be too dark to see, so turn on the TV and touch it again. Activate the door, use it, then use the elevator to go to the cafeteria. Talk to the chef about the battery to get Big battery.
Battery
Find the battery.


Go to where the penguin is and use the battery on the machine next to the penguin.


Ride the train.
The hole in my heart
Complete #1.

Keep on heading west until you see a train schedule board and a red button next to it. The button is the emergency stop. Push it.

Head upstairs. Head all the way to the west until you see a machine. Touch it and head to the east, passing through the fishes to head upstairs.

Head west until you see an ATM machine. Touch it to see Caselli, the penguin, drops something. Interact at that spot to get Penguin coin.


Coin
Find the penguin coin.


Head downstairs twice and then east. You'll see a vending machine after passing the first penguin. Use your coin to get Shrimp jar.


Shrimpster
Find the shrimp jar.


Use the shrimp with the R button and head upstairs. You don't need to lead this penguin to the exit, just lead it enough to let you pass to the stairs. Use your newly acquired Shrimp jar to keep on heading east until you see another penguin, sleeping. Interact and touch with the cone next to it to get a glimpse of its boss.


The red penguin is the second penguin to the west. Use your Shrimp jar to lure it to the sleeping penguin. Now, lure the sleeping penguin with the Shrimp jar to the machine in the far west.

Feed the penguin with your Shrimp jar (use the R button instead of interacting with it).
Junk food
Caution: do not feed the animals.


Head to the third floor and exit the station. Follow the path until you see a dog. Keep on heading east until you reach a dead end, and a vending machine. Touch the vending machine. Interact with the pot and move it to the left.


Enter the alley. Activate the door, but don't enter it yet. Keep on heading east to find the dog. There's no memory that you can check here, but you'll find a bone if you interact with the big, white flower near the door that is leading to The Whale.


Use the door to return to The Whale and sleep. You'll notice a game that is in the room after you woke up. Just keep on pressing your action button to start and win the game.
Level 1 - Can't even read
Play against 195.


Head downstairs, to the cafeteria. Ask the chef for some meat to get Chicken drumstick.
Chicken drumstick
Find the chicken drumstick.


Return to the dog in the alley. Take out the meat and get close to it. Interact and touch with the bicycle to the east.


Get out of the alley to return to the shopping district. Interact with the spot that you saw in the bicycle's memory to unlock a door.


Head east from the turtle to find a sign. Interact and touch it.


You'll learn that the turtle is attracted to shrimps. Put some shrimps near the pipe on the far east and get on top of the turtle. The water supply in the turtle's back will be used to unlock the door on the other side eventually and you'll be able to go to the door after the turtle moves to the west. Enter the room.

The next room is a bit tricky. You need to fill the water again with the turtle, but you need to check how much you need to fill it. Bait the turtle with shrimps until you can stand on top of it and touch the meter at the other side. Fill the water until you set the meter on the same position as the one in the memory. You can use the button to lower the meter count. Head to the next room once you're done. Note that you can lure the turtle with shrimp when its water tank is still empty if you fail to reach on top of it afterward.

After the cutscene, head to the next room. You'll need to head to the previous room and touch all of the pumps to figure out the puzzle.





Hint: check the order of the light
Solution: turn the pump in this order: 3-2-1-4.

Golden whistle
Find the golden whistle.


What big eyes
Complete #2.

Use the whistle. You can press R to let the dog run and press R again to let it stop and change direction. You need to wait for a while after it stops before it changed direction though. Let the dog run to the far east to pick up an item. Assign it to go in front of you so you can interact with it and pick it up.
Handle
Find the handle.


Use the handle to the place where it was shown in the memory. Tighten the wire. Use the whistle again to command the dog to head upstairs. Stop when you reach a ladder to knock it down. Once you use it to head up, touch the dog.
The fluffiest boy
"How long are you going to keep petting me?"


Follow the path to the east until you reach a dead end. Interact with the object near the cliff to extend the path.


Enter the room. Touch the pot to get the general layout of the room. See where the lever is? Pull it down.


The room should light up. Pull the lever on the east corner down to allow the dog to reach the top. Before you exit the room and do that, pull the west lever, the one that you used to turn on the light, up. A rain will start pouring out after the dog is on the top. Loosen the wire near the big, white flower to let the water reach it to reveal a ladder. Climb it and head to the east exit until you reach The Mirage Library.

Enter the library to find that it's closed. Climb up to find a door that is leading to The Whale. Activate it and enter it to play another game with the traffic light. You'll get an achievement if you win.
Level 2 - Getting used to it
Win against 195 after he improved.


Return to the library and use the exit to the east. Shake the tree. Head to the library entrance to touch the apple. Move the basket to the place the apple was and shake the tree again. Before you take the apple, battle with the traffic light again in that console game.
Level 3 - Moving smoothly
Win against 195 after he gave his best.


Return to the library. Before going to the library entrance, pull the lever down first. Push the basket to where the guard is and enter the library. You should be able to access the library section now.

The library section is a stealth area. You must be careful to not being seen. Your objective here is to find 2 books: red and yellow. The first one is right next to the first guard.
Red book
Find the red book.


Return to the shelf with red books west of the first guard. Use your red book to push the shelf to the right. The yellow book is on the small stairs on top of this shelf.
Yellow book
Find the yellow book.


Take out the red book and continue traversing the area. You'll see another stair with yellow book shelf in it. Put the yellow book and climb the stairs. Touch the blue shelf on the top and put the red book. Walk all the way to the east to find another guard. Talk to it to find some clues. Now, return all the way to the first shelf in this area, taking out all of the books along the way. Use yellow book on the shelf to find a hidden door. Enter the room and touch the chair to find a clue.

Return to the area with the apple tree. You need to pull the lever up first to reach it. Touch the mug to see another clue. Enter the stealth section again after pulling the lever that leads to the apple tree area down. Take out the yellow book in the first shelf and go to the place where the rabbit with a table was. Put yellow book on the shelf it was standing on approach it from behind. You'll get Locker's key after examining it.
Locker's key
Find the locker's key.


Examine it again to get another achievement.
All things fluffy
A fluffy challenger appears.


Take out the yellow book and use it to reveal the hidden door you accessed previously. Enter the right locker and use the golden whistle to chase off the guard. Unlock the left locker with your key to get dressed as a guard. Exit the room.

Head past the guards and touch the golden shelf. Put the blue book inside. Use the elevator. Touch the newspaper article, and then read it after the cutscene. You can read the yellow book by pressing R to read about the manual for the console game in your room. Once you are done, head upstairs.
A quantum of truth
Complete #3.

Play the console game again with the traffic light. Win it to get an achievement.
Level 4 - Learning tricks
Win against 195 after he learned new strategies.


Touch the couch and plant near the blue door. Exit the Whale and head to the area where you first meet the traffic light. Examine the dark tree on the way to where you touch a blue shoe for the first time for an achievement. You also can read the news article near the traffic light if you want.
Intreesting trees
What's this tree?


Return to The Whale and head to the cafeteria. Touch the table and interact with the couch.


Blue book
Find the blue book.


Return to where the dog was by using the door in your room to the back alley. Talk to the dog and head to the library entrance, but don't go inside the library. Instead, head to the east exit. Activate the door on the way to the exit. Read the sign near the exit and talk to the guy blocking it to get Painting brush.
Painting brush
Find the painting brush.


Use the brush at your inventory and press R to the canvas. Return to the library entrance and memorize the apple that you dropped earlier. Return to the canvas and draw the apple. Press R again on the canvas to erase the painting. Talk to him again after the cutscene for a side quest.

Return to The Whale and memorize the exit sign leading to the train.


Return to the skull and draw the sign. Talk to him about the game again for your next quest. Go to the place where the dog is, back alley, and memorize the symbol near where the dog stand to activate the water.


Return to the skull and draw the sign. Talk to him about the game again and go to the shopping district, accessible from the back alley. Memorize the water symbol in the pump station entrance.


Return to the skull and draw the sign. Talk to him about the game again and go to The Whale. Memorize the symbol in the device.


Before you return to the skull, run the console game in your room. Press the secret code that the skull said on the title screen, right after the logo stopped moving: up up down down left right left right.
Burst
Unlock card.


Return to the skull and draw the sign. Talk to him about the game again and go to the shopping district, accessible from the back alley. Memorize the fish symbol next to where you memorized the water symbol.


Before you return to the skull, run the console game in your room. Press the secret code that the skull said on the title screen, right after the logo stopped moving: left right right right down up up right.
Electrosaber
Unlock card.


Return to the skull and draw the sign. Talk to him about the game again and head to the east exit.

Head upstairs and enter the room. This is a labyrinth. It'll be easier to notice where to go if you use your brush, but if you're lazy and just need the solution, here it is: down up up. Once you exit the labyrinth, head all the way to the east exit. You'll see a door that leads to the storage room. Touch all the canvas and activate the door. Use the door and play with the traffic light again.
Level 5 - Machine learning
Win against 195 after he used machine learning.


Return to the museum through the door and exit the room for a cutscene. Enter the labyrinth again from the right side and head to the west exit. You'll be in the midway exit. Touch the poster to your left. You'll notice that there is a walkable path to the east exit. Examine the planet images first before going there though. Memorize the planet after matching it with the painting that you touched. Head to the east exit afterward to see the museum's layout. Return to the labyrinth and draw the image on all of the path leading to the top (second screen). Exit the museum.

Head all the way to the west to see another image near the west exit. Memorize it and draw it in the first labyrinth room. Follow the ant to the storage room. It will stop at the third room, saying something about a mark. Touch the top canvas to see an exit sign next to it. Exit the labyrinth to see an exit sign. Memorize it and draw it next to the canvas (not on the canvas).



Enter the storage room. Memorize the "staff only" sign.


Return to the skull and draw the sign. Talk to him about the game again for an achievement.
VOLTA pro
Make Scull remember all about the game.


Talk to him before leaving this area to get another achievement.
The brush's SOUL
"I wonder how my chum's doing."


Return to your room and run the console game. Press the secret code that the skull said on the title screen, right after the logo stopped moving: left up right up down down down down.
Overclock
Unlock card.


Return to the storage room and head all the way to the east for a cutscene.
Preparations
Complete #4.

Battle the traffic light again in the console game.
Level 6 - Annihilation
Win against 195 in annihilation mode.


Before you enter the musem's storage room, feel free to talk to the skull on the way to the museum entrance for some revelations. Head to the museum's storage room, to the place where the train is located. Exhaust the dialogue with the food storage and the penguin every day. You'll get three achievements on the second day.
She thought of everything
"This bread has unlimited shelf life. It's literally as hard as a diamond."


Weird dreams
"You're going to love tomorrow's story," or something.


Great engineer
"......"


Keep on interacting with everyone and sleep until you got out of the train. Head east afterward to find a red marble. Examine it to get Red marble. Follow the west path and examine everything that you see. The rest of the path is pretty straightforward.

You'll eventually reach a classroom. I'm not sure whether the achievement will be granted here or not, so I'll just leave it here.
Confrontation
"Miss Sakura, is that you...?"


You'll have two choices: stay or leave. The ending branches here, so if you want to choose the bad ending, go towards the person. You won't be able to load your save this way, but the game will have an extra save point that you can load before this point, titled "#9 Spare save (before branch)".

Load your save and choose the other choice if you get this ending. Before you move, bring the Red marble out of your inventory. Use it with the R button when you can't move your body. A scene will show up if you do this correctly and saved you from the bad ending.

Touch the utility pole to end the chapter.
To the rescue
Complete #5

Win the console game against the traffic light.
Level 7 - Apocalypse
Win against 195 in apocalypse mode.


Head to the train station in the Whale and enjoy the scenery on the far left.
Blue
The color of this beautiful world.


Exit the hotel and go to where you meet the traffic light for the first time. Head west to get Blue shoes.
Blue shoes
Find the blue shoes.


Press Q, then W to read your chat log. Press shift+W to read the oldest log. Exit the chat log and enter the area through the railroad. Follow the path until you see an opened door. Head inside. Again, follow the path until you reach a dead end. Interact with the plank to touch it.


Pull the lever down to unlock the second floor. Head upstairs and exit from the door to the west. You'll see a lot of levers. Pull the first one down and head upstairs. You'll see a lot of golden statues to the west. The middle one is empty, but it says that it's a golden fish.


The truth is, you can move some part of the statues around after you read the description of the middle statue. Solution: push the left statue to the right and the right statue to the left. Before you memorize the fish statue, pull the lever next to these statues down to unlock the fourth floor.

Memorize the fish drawing and draw it on the canvas in the second floor. The fish will move and you'll be able to pull the other lever outside of this room down. Head to the fourth floor. Look, a turtle! Before you move the turtle that is standing on the far west, interact with the shiny object next to it.


Take out your golden whistle. Use it and Bern, the dog, will come. Guide it to the top floor, up to the platform with stairs. Leave it there and lure the turtle to the dog's location. Arrange it so that the dog will stand on top of the turtle to get the item that you found on the far west. Take Lab's key from the dog afterward.

Return to the second floor and use the key to the door. Exit the lab from the east exit. Touch the plank and pull the lever. Head to the fourth floor and guide the dog to the rightmost pipe. You'll be in an area with a pushable block. Push the block to the second pipe from the right. You should be able to water the plant from the pipe this way. Lure the turtle to the rightmost pipe.

Climb the ladder and ride on the turtle when it's going to the west. Walk all the way to the west to get an achievement.
Red
The color of this melancholic world.


Bait the turtle again so that you can ride on top of it. Drop on the top of the building west of the stairs. There is another stairs that will lead you to the third floor. Use it and head to the far east for a cutscene.
Our promise
Complete #6

Keep on heading to the east and you'll get an achievement after you learn everything.
Reunion
"I've come to see you."


Note that the story will branch off again here. In order to get the bad ending, simply exit the building and meet Miss Sakura in road 195. You'll get an achievement for it, so if you're a completionist, you might want to do this first.
Paranoia
A cliché ending, isn't it?


Just like before, the game will set up a checkpoint before the story branches. Load your save. Before you leave the building, stop by on the third floor and memorize the horn statue (right statue). Make sure you fix the statue to the state before you draw the fish. Touch the chalkboard that is located in the lab, located in the second floor, twice before going to road 195.

Fish ticket
Find the fish ticket.


Talk to Miss Sakura again after you reach road 195.
Obsession
" "


Talk to Cullet, the owl.
The crow's friend
"Did I make you worry, Cullet?"


Examine the dark tree next to Miss Sakura.
Intreeguing trees
"An undefined tree."


Return to the Whale and go to the cafeteria. Head to your room and win the last console game with the traffic light.
Level 8 - Optimization
195 optimized his program for playing against friends.


There is another secret code that you can put into the game to get an achievement and a card, but you can't input it in the game after you learn it. If you don't want to reload previous chapters after finishing the game (we'll have to do this for 4 other achievements btw), input up right down up up down right up to get your last card.
Beam
Unlock card


Visit the engineer mouse afterward to repair the door in your room. After you moved to the back alley, talk to the dog, the skull in the museum entrance (draw the horn you memorized in the school to get your last card code), and the planet head in the museum. Head to where the train in the museum was and talk to the moss-like creature there to get an achievement.
A familiar face
"What are you doing here? Go away."


Head to the train station. You can enter the station again with the Fish ticket you got from the fish in the school. Use the elevator once and head all the way to the east to find two sleeping penguins.
Sleep tight
You must be tired.


Head to the lowest floor. You'll eventually get another achievement.
A journey through memories
Complete #7

Return to Miss Sakura and ask her to return to the reality. Use your blue shoes from the inventory with the R button. Once you reach the end screen, you'll get an achievement.
Unreal Life
You're going to love tomorrow's story.


The "last" achievement will be obtained after you reach to the title screen.
Azure
The color of this cruel world.


Congrats for beating the game!

Now, it's time to get your remaining achievements. There should be 4 (or 5 if you didn't put the last card code). Load the third chapter and continue the game until you get Locker's key. Examine the guard with the key for a second time before leaving.

If you haven't inputted the last console code, head to your room and input up right down up up down right up to get your last card.
Beam
Unlock card


Remember the locked locker on the Whale? You can reach the area west from the lobby. Keep on using your locker key on the locker until it fits.


Singularity
It couldn't be a coincidence.


Continue playing the game until you reach the museum. You don't have to do the optional quests like playing the console game or drawing random signs to the skull. Do a manual save after you reach the museum's storage room, before you end the chapter (right after Hal says "A secret...?"), and DON'T replace it. Ever.

Continue playing the game normally until you reach chapter 7. After you exit the school building and asked Miss Sakura to say farewell with everyone, enter the locker in the Whale. It's a long walk, but you'll find a weird cat inside. Talk to it.
A weird cat
"The pleasure is mine, familiar feline."


Load your manual save. Head to the locker room in the Whale before ending the chapter. You'll eventually see the moss-like chef inside. DO NOT talk to it. Instead, keep on heading west to find some papers. Read them all to get an achievement.
The truth
It was the truth that found you.


Now, talk to the moss-like chef inside the locker. Continue playing the game until you reach the true ending. There will be some additional scenes after you leave the Whale for the last time and after you return to reality.
A causal exception
Too many unfolding roads.


Feel free to close the game after you get the achievement since there's nothing new with it.

I'm pretty satisfied with the guide. The extra achievements in the cleanup section is quite annoying to get - I spent a lot of time just to unlock the locker before examining the bunny guard for the second time, and after I did, the locker sort just unlocked itself after a few tries. I wish I had do that earlier... The rest of the achievements are also annoying though, especially since you can't skip the cutscenes and puzzles. There's only small amount of extra info that you can get (mainly the one in The Truth achievement), so it's kinda not worth the extra playtime.

Anyway, enough with my rant. Hope you enjoy the game!

Achievement guide by Dieusino and comment from Harle
sudzzuds's and Nixmachine's comment in Full playthrough of the game (in case someone needs help) contain spoilers
megaomnislash's comment in Asking for help with remaining achievements - mild spoilers included !