100% Completion Step-by-Step
After going through the game, well, hundreds of times in the process of making my flowcharts, I decided to try and put together a "shortest route" to 100% completion. Here's what I have come up with, including save management. This covers all of the scenes and all possible endings, with the "bad" endings for each girl coming before the better ones.
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* Prologue
Out Cold
Bundle of Hisao
* Act 1: Life Expectancy
Gateway Effect
Yeah, of course.
Enter Stage Left
In the Nursery
Ask about the library.
Nobody's Room
Smalltalk
Risk vs. Reward
She has a point. Attack aggressively!
Psueduo Tea Cosy
Shared Library
I'm sorry, I didn't mean to startle you.
Bizarre and Surreal
She was cute.
Lunch Evolution Theory
SAVE at decision screen (Create a new save state)
Go talk with Hanako.
Meet Cute
Sip (Part 1)
It Builds Character
A Private Lunch
Waylay
Maybe.
The Other Green
The Running Girl
Soap
Cold War
Hey, come on. Cut me and Lilly some slack...
Above and Beyond
Paint by Numbers
Invisible Hat
No Recovery
Foot and Mouth
Mind Your Step
SAVE at decision screen (Create a new save state)
I don't really want to talk about it.
Support
Don't Panic
The Deep End
KENJI'S ENDING <<<
LOAD "Mind Your Step"
Sorry, I'm not in very good condition.
Support
Sip (Part 2)
SAVE at decision screen (overwrite "Mind Your Step")
Go for a walk into town.
Don't Panic
Promise of Time
* Act 2: Past
Earl Grey
A Pound Sterling
Presents and Presence
Unidentified Drinking Object
The Day After
A Brief History of Thyme
Tell the truth.
Little Wing
Bon Voyage
* Act 3: Present
Day by Day
Minor Discord
Humor him.
Ask about Hanako.
Dissonance
A World Away
Renewal
Northern Sojourn
Prelude
Address it.
Crescendo
Diminuendo
Gray Outlook
Rhapsody in Blue
* Act 4: Future
The Momentary Present
Talk about Hanako.
Slow Steps 'Fore a Waltz
Pajamas and Suits
Correct Procedure
Out and About
SAVE at decision screen (Create a new save state)
Drop the subject.
A Morning's Reverie
Blackout
Context
A Faraway Future
Farewell
LILLY NEUTRAL ENDING <<<
LOAD "Out and About"
Mention the letter.
A Morning's Reverie
Blackout
Context
A Faraway Future
Farewell
False Cadence
Under a Maudlin Sky
Under a Bright Sky
LILLY GOOD ENDING <<<
Forwards, with Gusto!
LOAD "Sip (Part 2)" (You may now delete "Out and About" save)
Go to the library.
Don't Panic
Nc5xb3
Movement
* Act 2: Hide and Seek
To Town, To Town
Tea Leaves
SAVE at decision screen (Overwrite "Sip (Part 2)")
What do you think, Hanako?
Office Confessional
STOP at "Rise and Shine"
LOAD "Tea Leaves"
I've done enough work for the council already.
Chess and Slides
Rise and Shine
Mad Hatter
Small Change
Absenteeism
Equivalent Exchange
* Act 3: Castling
Invitation
Shady Encounter
Admit it.
Antiques and Pie
Falling
Treading Softly
Reaching Out
One More Year
One Piece of Paper
Stripes and Solids
Beginning of the End
SAVE at decision screen (Overwrite "Tea Leaves")
How about we call it a day?
* Act 4: Scars
Truancy
Faraway Presence
Trust my own judgement.
Misstep
HANAKO BAD ENDING <<<
LOAD "Beginning of the End"
Do you want to go into the city?
* Act 4: Scars
Truancy
Faraway Presence
SAVE at decision screen (Overwrite "Beginning of the End")
Trust my own judgement.
Cut Petals
HANAKO NEUTRAL ENDING <<<
LOAD "Faraway Presence"
Agree with Lilly.
Continuing Melody
Shanghai Studiousness
His Past
City Rendezvous
Whispered Touch
Indeterminate Future
Adulthood
HANAKO GOOD ENDING <<<
LOAD "Lunch Evolution Theory"
Wait for Shizune and Misha to come to a decision.
Short Sharp Shock
Detour Ahead
A Private Lunch
Waylay
Yes.
The Other Green
The Running Girl
Soap
Cold War
SAVE at decision screen (Overwrite "Lunch Evolution Theory")
Hey, come on. Cut me and Lilly some slack...
Above and Beyond
Things You Can Do
Exercise
Take it easy.
Invisible Hat
No Recovery
Foot and Mouth
Mind Your Step
Sorry, I'm not in very good condition.
Support
An Aesthetics
Creative Pain
I'm interested in the art club.
Don't Panic
Clouds in my Head
* Act 2: Disconnect
A Wider Field of Vision
Studies in Grayscale
You're Amazing!
Interstitial
Self Study
Hisao's Smile
Things You Like
It makes me feel like I'm stuck.
Target Audience
Eternity in an Hour
Underwater and a Maple with a Name
I want to be more like Rin.
Iwanako's Regret
In Her Own Image
SAVE at decision screen (Overwrite "Faraway Presence")
I think you'd be a big hit.
Umbrella Logic Cake
Six Meters Closer to Heaven
Indecision
Signal Interference
Dandelions
What about Emi?
* Act 3: Distance
22nd Corner
The Scent of Light
Things you Can't Give Up
BADAAN!
I can't leave her alone either.
STOP at "The Edge of the World"
LOAD "In Her Own Image"
You won't get a chance like this again.
Umbrella Logic Cake
Six Meters Closer to Heaven
Indecision
Signal Interference
Dandelions
What about me?
* Act 3: Distance
22nd Corner
The Scent of Light
Things you Can't Give Up
Rose-Tinted Glasses
I want to support her.
The Edge of the World
The Context of Rin
Fast Forward
Self-Destruction
Reverse Escapism
Boundless
Is that why you're being so supportive of Rin?
Delirium
Things You Hate
SAVE at decision screen (overwrite "In her Own Image")
Then explain.
Shards of Ire
RIN BAD ENDING <<<
LOAD "Things You Hate"
It doesn't matter.
* Act 4: Dream
Illusions for People
Demised
The Scene
SAVE at decision screen (Overwrite "Things you Hate")
But aren't you happy people are interested in your paintings?
Wavelength
Blue Period
The World Only You Can See
RIN NEUTRAL ENDING <<<
LOAD "The Scene"
But if you found someone like that, then what?
Desperate Glory
Problems of Self-Referential Logic
Measuring Shadows
Raison d'etre
Without Breathing, Without a Sound
Proof of Existence
RIN GOOD ENDING <<<
LOAD "Cold War"
Don't drag me into this! I've done my part!
Proof of Competency
Event Horizon
Exercise
SAVE at decision screen (Overwrite "Cold War")
Take it easy.
Invisible Hat
Home Field Advantage
Try to dodge the subject.
No Free Lunch
Shanghaied
Don't Panic
Throwing Balls
* Act 2: Learning to Read
Message Passing
Talk to the Hand
Chinese Whispers
Advanced Game Theory
Bread, Scissors, Paper
Interlace
Spring Into Action
Past Imperfective
When Stars Embrace
* Act 3: Sleight of Hand
Force Feedback
United Nations
Use-Mention Distinction
Family Plot
Pangrammatic Window
Closer
Confrontation
The Anchor
Roadmap
Acute Triangle
Dewey Decimated
Tongue-Tied
SAVE at decision screen (Overwrite "The Scene")
Comfort Misha
Look Aside
* Act 4: To My Other Self
Grand Strategy
Off by One
Invasion
Parfait
Present Tense
Spiral
Terminal
SHIZUNE BAD ENDING <<<
SAVE LOAD "Tongue-Tied"
Refuse.
Look Ahead
* Act 4: To My Other Self
Grand Strategy
Off by One
Invasion
Parfait
The Summit
Succession
Sneaking Mission
Infinity
SHIZUNE GOOD ENDING <<<
LOAD "Exercise" (You may now delete "Tongue-Tied" save)
Go for it.
Slow Recovery
I don't want to talk about it, okay?
I'll go to lunch with Emi and her friend.
Foot and Mouth
Support
An Aesthetics
Proper Exercise
Don't Panic
Is Carnival!
* Act 2: Form
Morning Run
Clouds, Time Travel, and Thou
Questions That Need Answering!
Second Time's the Worst
An Apple a Day
Track Meeting
Down that Medicine Now
Piracy on the High Seas
Famous Last Words
Offer to run with Emi.
Tracking absences.
Dropping By
The First Morning After
The (Real) Beginning
* Act 3: Perspective
Eet Ees... Scienca
Definitions
Let it rest.
Invisible Rock
Lunch and Science
Up, Down, and Up Again
Storage Space
After-School Plans
Detached
Phantom Pain
I Suppose I can spare a few minutes.
Debate Expresses Doubt
Sure, why not?
Guess Who's Coming... Never Mind
SAVE at decision screen (Overwrite "Exercise")
Go after her.
Instant Replay
SAVE at decision screen (Create new save state)
Downplay the issue.
EMI BAD ENDING <<<
LOAD "Instant Replay"
Give in and let Misha know
STOP at Act 4 splash screen
LOAD "Guess Who's Coming... Never Mind"
Talk to her mom.
* Act 4: Motion
A Swing and a Miss
Saving Throw
Whispers of the Past
Hooray for Socks
Clean Teeth
EMI GOOD ENDING <<<
> Delete "Instant Replay" save
> DELETE "Guess Who's Coming... Never Mind" save
I just deleted my own save file (tearfully, and after backing it up) and tested the walkthrough, and sure enough I have 100% completion and everything in the Extra unlocked again!
Edit: Thanks to eldorin for helping make sure this is 100% complete.
Edit 2: I've now updated Rin's route to add a save point in "Things I Hate" to avoid replaying the entirety of Act 3 multiple times for no reason. The guide is still fully complete, but quite a bit faster in that section.