Homura's wish also seems to be linked to Madoka, given how Homura believes a MG can only fight for her wish, and Homura seems to only fight for Madoka.
My theories are either she comes from the future and want to help out Madoka, or she comes from the distant past and madoka is the reincarnation of someone she wished for.
In that case, she may predate Kyuubey.
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