Puella Magi Madoka Magica the Movie Part 2: Eternal

Madoka learns from Kyubey, whose real identity is Incubator, that his species makes contracts to make girls into magical girls that inevitably become witches in order to use the energy that spawns from their despair to counter entropy in the universe. Kyouko, hoping for a chance that Sayaka can be made human again, takes Madoka with her to try and reach her humanity. This ultimately fails, with Kyouko choosing to sacrifice herself to destroy Sayaka with her. Meanwhile, it is revealed that Homura comes from another timeline, having relived the same month several times in the hope of saving Madoka from a grim fate at the hands of the ultimate witch, Walpurgisnacht. Homura attempts to face Walpurgisnacht, but is ultimately defeated and draws close to despair, feeling her efforts have become pointless. Just then, Madoka appears and uses the built up energy from several timelines to become a powerful magical girl capable of eliminating witches before they are born.

Synopsis from Anime News Network