Chapter 1: Look At Me
The third timeline is the first wherein Sayaka makes a contract, and this is when Homura learns to keep an eye on her.
“I’m fine!” Homura remembers her saying after the two of them and Mami killed the witch whose whole barrier looked disconcertingly like a child’s drawing. “I took care of myself when I went out with Madoka yesterday evening.” (Later, Madoka would mention that they had only fought minions that night. Homura would think it odd, but neglect to pursue that thought.) When all five of them were together in a group, it was always, “I took one down before any of you even got here. Way to keep up!” or, “No worries, I barely got to use any magic in that fight. You guys need to stop hogging all the shots!” Homura doesn’t put it together until the day before Walpurgis, when Sayaka suddenly slumps to the floor.
“Oh,” she says, her voice strangely empty. “So that’s what happens.”
Kyouko runs to her. Madoka tries to do the same, but Homura grabs her wrists and restrains her. “Get back!” she calls out. “Her soul gem is about to explode!”
Kyouko disregards her and kneels down over Sayaka. “Whaddya mean ex—” Then she gets it. She lifts Sayaka partly off the ground by her shoulders and shakes her. “You idiot! You haven’t been cleaning your soul gem!”
Sayaka smiles weakly at her. “You had a point about there not being enough grief seeds to go around for a group this size. I couldn’t just let you be right about that. Warriors of justice always have to rely on the power of friendship.”
“So is that what’s going to fix you, huh?!” Kyouko shouts at her. “You got a plan for how we can use the power of love and friendship to make you better, or are you just going to die here?”
“It doesn’t really matter, does it?” Sayaka asks, and there’s something different in her voice now, something almost insubstantial: thin as the edge of a sword, but just as sharp. “Mitakihara doesn’t need me; I’m useless compared to the rest of you. Mami keeps saying I’ll get better with experience, but even Madoka is stronger than me. Besides, I’m not the kind of person that the power of love works for.”
“Don’t say that!” Madoka calls to her, tugging feebly against Homura's grip. Homura instantly feels so horrible that she almost lets her go, but forces herself to harden her heart and hold on. She’s just glad she doesn’t have to see the tears she knows are streaming down her friend’s face, because Madoka is so kind that this must be killing her. “All of us love you and care about you so much, so don’t say something like that!”
“Then why didn’t you notice what I was doing?” Sayaka asks, and now it’s clear that she’s wielding her words to cut. “Why didn’t you even look at me? Why—” Her voice catches in a sob. When she speaks again, it’s with the force of water bursting through a dam. “Why does no one ever look at me?”
She dies in Kyouko’s arms, and the blast that throws Kyouko back nearly takes her arms off.
Chapter 2: Black and White, Red and Yellow
She can’t say it doesn’t surprise her, but it does make sense that a corrupt magical girl would turn into a witch. Sayaka said herself that Kyouko and Kirika were almost as bad as witches, so when Kirika sheds the “almost” along with her human body, she is one of the first, alongside Homura, to push through the shock and attack her like she would attack any other monster.
It’s a hard battle. Kyouko and Mami are clearly dazed. She’s a little dazed herself, and aside from that, she still doesn’t have much experience. Homura pulls them through, though, and for a moment Sayaka thinks that it will somehow be okay. It’s not that much worse than already being a zombie. They just have to be more careful with grief seeds and their soul gems, and maybe start carrying cyanide pills or something.
Then Mami shoots Kyouko and turns the gun on her.
“Why?” Sayaka whispers, falling to her knees.
“I love my kouhai too much to watch that happen to you,” she babbles. There are tears streaming from her eyes and there is mucus trickling down her upper lip, and her whole face contorts under the strain of the grief. Sayaka would never have believed that graceful Mami with her golden curls would be so ugly when she cried. “I’m sorry, I’m so sorry—”
Before she can pull the trigger, her soul gem shatters. For a moment, pink mist and gleaming shards of yellow crystal hang like a halo in the air around her head. Then she crumples to the ground.
Homura, who a second ago had been on the other side of the room, stands gun in hand less than a meter away from the body. “Are you all right, Sayaka?” she asks.
Sayaka realizes that Homura shot Mami at point blank range and feels an inexplicable rage prick at her heart. “Murderer.”
“She was going to kill you,” Homura says, as though it were something small enough that it could just be said, as though it were something light enough that it could travel through air as feather-thin words and not heavy enough to crack the world open like a hammer coming down on a blue ceramic bauble.
“She would never!” Sayaka sobs. “She would never hurt me or anyone else! Mami is good!”
“She killed Kyouko.”
“No! That’s backwards!”
Homura walks calmly up to her and just as calmly backhands her across the face. “Wake up! You saw all of it with your own eyes.”
“No,” she says again, but she isn’t really arguing with Homura. She’s arguing with reality, because reality is wrong. It’s wrong and it hurts, and even without looking she can sense that her own soul gem, already dimmed from the fight with Kirika, is growing steadily darker. “You’re already a murderer, so kill me too!”
“I can’t do that,” Homura says.
Sayaka lifts her sword and swings it at her. She vanishes and reappears a few meters away.
“Pull yourself together,” Homura says. At last she’s beginning to sound upset, and Sayaka takes a small measure of comfort from that. “I need you to help me fight Walpurgis Night. You’re probably not strong enough yet for it to work, but we have to at least try.”
Sayaka gets to her feet and charges her.
She’s right by the body when the bullet hits her. She feels herself falling, and the last thing she sees is a blur of yellow and red.
Chapter 3: Pocky
Based off of my favorite page of the manga.
“Almost!” Sayaka shouted, spraying a few crumbs with the intensity of her exclamation. “We’ll get it next time for sure.”
“This is so stupid,” Kyouko grumbled. “You’re stupid.” She pulled another stick from the bag and held it out anyway.
Sayaka regarded it critically, reviewing her strategy. On the first try, she had been too hesitant and choked on what was still in her mouth when Kyouko reached her. On the second try, she had been too aggressive and accidentally bitten the other girl’s lip. Last time, they had both been a little overeager. “There’s nothing here but the two of us and some pocky,” she said, gesturing frenetically at the white void around them. “What else are we supposed to do while we wait for something to happen?”
“We could make out like normal people, if you weren’t set on being such a weirdo.”
“I’m not a weirdo, I’m a romantic! And we can do that too, but first we’re going to get this right.”
Kyouko rolled her eyes.
Sayaka leaned in and pressed her lips around one end of the stick. “Come on,” she said out of the corner of her mouth. “Let’s meet in the middle.”
Chapter 4: Beneath thy guidance reconciled
This beautiful but amorphous world Madoka has given to them probably won’t last forever. Nothing will, not even the universe, not even with a seemingly infinite army of Incubators stoking its fires. Even if she had eternity, she doubts she could ever learn to play like he did. Still, she has plenty of time to learn to play like herself.
When she needs an instrument, she finds one. She also finds a woman who is willing to teach her, a woman who once signed her life away for the ability to make music the way she’d dreamed. Sayaka knows that she’ll never play like her, either, but she can accept that. All she wants is to be good enough to be able to give a little beauty back.
Kyouko doesn’t like it at first. “What,” she says, “you’re not really still stuck on him, are you?”
Sayaka isn’t. She says nothing and keeps playing, because if only she can do what she’s trying to do, Kyouko will understand.
A bit into the third song, Kyouko’s scowl fades. “Hey, wait a minute,” she says, and starts humming along. After a few seconds of that, she breaks into a soft alto. “Thou canst save amid despair. Safe may we sleep beneath thy care, though banished, outcast, and reviled. Maiden, hear a maiden’s prayer—” Sayaka stops playing and stares at her, and she flushes. “What?”
“I never knew that it had words.”
“Of course it has words. It’s a prayer.”
“I also didn’t know that you could sing.”
“I can pray.” Kyouko’s flush deepens. “Though, it’s been a long time.”
“I see,” says Sayaka, smiling warmly at her. “I’m just learning. Will you pray with me?” She picks up where she left off, and, after hesitating a moment, Kyouko joins her.
“Ave Maria, undefiled. The flinty couch we now must share shall seem with down of eider piled, if thy protection hover there—” Sayaka breaks off again and begins to giggle. “What now?”
“Oh come on, that’s not really in it, is it?” Sayaka asks her. Kyouko just stares at her in confusion, so she clarifies: “Two girls sharing a couch?”
“What? No! That’s not what that means!” Kyouko’s face is almost as red as her hair now. Sayaka has a strange urge to reach out and pat her cheek, and that thought just makes her giggle more. “It’s a church song!”
“I don’t think she would mind though,” Sayaka muses. “I think she wants more than anything else for us to love one another and make each other happy. Maybe she’d even see it as another kind of prayer.”
“You’re so weird,” Kyouko grumbles. “Just start playing again before you drive me crazy enough to kiss you.”
Sayaka carefully places her violin back in its case and sets it to the side.