This guide is as spoiler-free as possible. It is a walkthrough for the important decisions you need to make to play the game with a linear, chronological narrative, but contains no plot or puzzle details.

Passwords are not included in this list for the sake of reducing spoilers. You will find every password before you need it, so write them down. Additionally, this list includes bad endings, some of which will be very obvious. Some bad ends are required triggers for future content, so don't attempt to skip them.

The walkthrough is not broken up in any way, to preserve the surprise of when a timeline is coming to an end. If you lose your place, see the endings section and hover over the spoiler that lists how many endings you have.

Several fragments include actual randomness. I have included a quick way to identify which branch you are supposed to be on in these cases. To avoid seeing content out of order, you should pull up the menu and return to the flowchart immediately if you realize you're on the wrong route. You do not need to wait for the segment to end.

First Choice -> Either (Random)
Any Team: Coincide (Only choice) -> Opposite answer
C Team: Execution (Only new) -> All three, Q
Q Team: Execution (Only new) -> All three, D
D Team: Execution (Only new) -> All three, C
C Team: First Come, First Saved (Bottom right) -> Press
You only have one choice at this point, play until you get a choice again.
Q Team: First Come, First Saved (Bottom left) -> Press
You only have one choice at this point, play until you get a choice again.
D Team: First Come, First Saved (Bottom right) -> Press
You only have one choice at this point, play until you get a choice again.
Q Team: Execution (3rd row, left) -> C
Q Team: Radical-6 (3rd row, middle) -> Don't
D Team: Outbreak (3rd row, right) -> Don't Run, Run
Q Team: Execution (3rd row, left) -> D (Yes, you have to redo it)
C Team: Execution (Top right) -> D
C Team: Suspicion (Top middle) -> Akane, Carlos
Q Team: Triangle (3rd row, right) -> Nobody, Mira, Eric
C Team: Execution (Top right) -> Q (Yes, you have to redo it)
D Team: Execution (Top middle) -> Q
C Team: Poison (3rd row, left) -> Wrong Answer, Correct Answer (Random, but solvable)
D Team: Fire (2nd row, left) -> Shoot Live (Random, retry if Phi says "Sigma...")
C Team: Anthropic Principle (3rd row, right) -> Lose, Win (Random, and yes, you really need to win, just keep replaying it until you do)
D Team: Fire (2nd row, left) -> Shoot Blank (Random, retry if Phi says "No... It can't be..."), Don't Drink, Drink
C Team: Ambidex (2nd row, left) -> Ally, Betray, Middle Branch
You only have one choice at this point, play until you get a choice again.
Q Team: Pop Off (Bottom right) -> At least one of [Eric, Mira, Carlos, Sigma, Gab, Zero, Me], Dunno
Q Team: Radical-6 (3rd row, middle) -> Inject
D Team: Suppression (Top left) -> Press, Don't
Q Team: Reality (2nd row, left) -> Refuse, Press, Left Branch, Right Branch
D Team: Fire (2nd row, left) -> Don't Shoot
C Team: Monty Hall (Bottom left) -> Don't Switch (Random, retry if locker is not empty), Switch (Random, retry if locker is empty)
D Team: Transporter (2nd row, middle) -> No, Yes
D Team: Transporter (Left)
D Team: Door of Truth (Only choice) -> Correct Answer
C Team: Get Back (2nd row, middle)
You only have one choice at this point, play until you get a choice again.
C Team: Apocalypse (3rd row, middle)
Q Team: Q (Top Middle) -> Wrong Answer, Correct Answer, at least one of (Sigma, Diana, Eric, Mira, Phi, Me, Gab), Real Name
Q Team: Triangle (3rd row, right) -> Real Name
OPTIONAL: Go back to each team's Execution fragment one last time and have C vote for D, Q vote for C, and D vote for Q.
C Team: First Come, First Saved (Bottom right) -> Don't Press
Q Team: First Come, First Saved (Bottom left) -> Don't Press
D Team: First Come, First Saved (Bottom right) -> Don't Press
C Team: Force Quit (Bottom middle) -> Correct Answer (Omit the space)
Q Team: Force Quit (Top left) -> Correct Numbers
D Team: Force Quit (Top right) -> Correct Answers (Include the space in the second one)
Any Team: Final Decision (All nine characters together) -> Don't Shift, Shift
Any Team: Coincide (Zero holding a coin) -> New Branch
Finally, check out the File section -> Post Payoff: Akane and Junpei, then Carlos, then Sean, Eric, and Mira

If you lose your place in the walkthrough, hover over the spoiler next to the number of endings that are displayed on your save file. Inside the spoiler is the decision that led to that ending. From there, you can check each fragment's flowchart until you find the decision you need to make next

1 Ending: First Choice -> Either

2 Endings: D Team: Outbreak (3rd row, right) -> Run

3 Endings: Q Team: Triangle (3rd row, right) -> Eric

4 Endings: D Team: Transporter (Left)

5 Endings: C Team: Apocalypse (3rd row, middle)

6 Endings: Q Team: Q (Top Middle) -> Real Name

7 Endings: Any Team: Coincide (Zero holding a coin) -> New Branch

There are a lot of these, too many to list here. The explanations behind the route are also full of spoilers, so I have posted them in the forums here.

Please keep any corrections and suggestions to that thread, so that this guide's page remains as spoiler free as possible.