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The first time, Sayaka and Kyouko do not meet.
Kyouko is heading to town and setting the stage for that to happen when Honmura resets time, putting everything back to where it was a month ago.
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There are times when Kyouko and Sayaka fight and distrust each other before they become friends. There are times where they're working towards friendship when Honmura arrives. There are times where Honmura can see the trust and love in Kyouko's eyes and wishes (maybe just a little) that she could wish for their happiness too. Only Honmura knows that's not the way it works.
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The second time, Kyouko gets there before everything goes to hell. She and Sayaka die together fighting a Witch, their fingers finding each other.
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Honmura stops counting after a while, because all the times are starting to get mixed up in her head, but the constants are this: Mami always dies, Madoka is always kind, and Sayaka has a habit of finding Kyouko, if Kyouko doesn't find her first.
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The third time, Kyouko punches Honmura for saying something a little bit mean to Sayaka. Kyouko had been there already when Honmura got to school, and Honmura doesn't really understand what's happened, but they're something like best friends.
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When Sayaka turns into a Witch the first time (this is after Honmura has learned the truth about Witches), Kyouko screams and tries to save her. Honmura holds her back, because a Witch is a Witch. Even if the Witch was someone you knew, even then.
They have to fight Sayaka.
In the end, though, all her efforts are useless because Mami goes crazy and kills Kyouko before Honmura can save her. Madoka's arrow pierces Mami's chest and thus, everything is righted again. Everything that should happen has happened, and Honmura thinks that maybe everything will go okay this time.
It doesn't.
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The fourth time, Sayaka and Kyouko are the kind of friends that pretend to hate each other but harbor a secret fondness for one another. Honmura thinks that may be the only good thing about this time when they die and Madoka turns into a witch that will destroy the world.
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It's always Sayaka that turns into a witch. Never Kyouko, never Mami. Only Sayaka and sometimes Madoka.
Honmura wonders why that is. She wonders if maybe there are Puella Magi marked for this task, marked to turn into witches for the next wave of girls filled with hope to destroy. Or maybe, Honmura thinks bitterly, this world created by those like Kyubey doesn't allow for happiness and splits people off. One girl must turn into a witch, and the other must defeat her.
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The fifth time Sayaka turns into a witch, she doesn't. Kyouko pulls her forward, kisses her, and drives her spear through Sayaka's chest. When Sayaka drops to the floor, Kyouko pulls her spear out, whispers I'm sorry, and drives it through Sayaka's Soul Gem.
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Sayaka is unstable. She doesn't listen, and Honmura can't stop her from becoming a Witch now. She's going to kill her, but then Kyouko is stopping her, because that's one of the things Honmura can't stop too. The whole world is falling to pieces, but it doesn't really matter if you have something to cling to, right?
Honmura can't even bring herself to be mad when Kyouko goes and kills herself to destroy Sayaka. It's how it should be, she thinks.
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The sixth time, Kyouko is at Mami's house for cake and Honmura's there to study. Sayaka pretends to be annoyed at Kyouko's presence, but she sits next to her anyway. Honmura thinks she's not the only one who notices, from the way that Madoka's lips tilt up just the tiniest bit.
That's the moment Honmura remembers the mostly clearly when she sets time back: the five of them sitting at Mami's little table and being friends. She wishes every time was like that.
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Madoka's wish is selfless. She wishes for something that no Puella Magi has before, maybe because she's the only one to know the full extent of the contract she's making, maybe she's the only one who has a view of the world pure enough to ask for something like this instead of a selfish wish like the ones all the other Puella Magi have made.
It changes the very fabric of reality itself, and when the wave of change washes over her, Honmura hopes that this new world will be like the one she liked best: friends eating cake and smiling. Even if that's not the case, she hopes everyone is happy because they deserve that after what they've been through (even if they don't remember any of it).
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The seventh time, Kyouko keeps trying to give Sayaka food. Sayaka refuses, because she thinks that Kyouko is merely trying to be her friend. Honmura knows better, though. She knows that Kyouko is trying to get Sayaka to like her back and failing miserably. She would intervene, but it's nice to watch the way they keep falling to together and then running away from each other.
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Honmura wakes up to a world that isn't the same, but no one knows that. Mami doesn't die this time, but Sayaka does. Kyouko doesn't speak for days, and Honmura thinks about telling her that it's okay because Madoka saved her and she's safe now, but she knows it won't help. No one in this new world knows who Madoka is, and they'd probably just think she was crazy.
Instead, Honmura just buys Kyouko a bag of apples and sits in the park with her, eating in silence.
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The last time, or maybe a time which doesn't exist, Kyouko's got her arms wrapped around Sayaka's neck, leaning forward with her face pressed to Sayaka's. They're laughing, and Honmura smiles, lifting the camera in her hands to take a photo of them together.
Mami peers over Honmura's shoulder at the picture, "It kind of seems like they were made for each other, doesn't it?"
"They were," Honmura says, slipping the camera back into her pocket, "They just don't always realize it."