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 four 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 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.