After defeating Oktavia herself, Kyoko decides she doesn't want to fight with Homura against Walpurgis because she will not fight with someone that killed Sayaka. Mami has killed herself because she doesn't want to turn into a witch, and so Homura is the only one left to fight Walpurgis.
Madoka comes in Homura's room one day before the event, and Homura explains everything about Kyubey, the Witches, and why she became a magical girl. When Walpurgis is there, Madoka wants to help Homura, but she says that she is her only hope left, so she has to survive.
After defeating Walpurgis, Homura is severely wounded. Madoka wants to help her, but she refuses, saying that she has looped countless timelines to see one where she is alive. Madoka says Homura is her only friend left, and pleads her not to leave her alone. Homura assures that she'll be fine as she still has her family.
Homura thanks Madoka for letting her save her and being with her until her final moments, and passes away. Kyubey comes by, complimenting Homura for being able to defeat Walpurgis by herself, but notes that with no magical girls left to protect Mitakihara, he only needs to wait until another disaster strikes to force Madoka to contract with him.
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