Having recovered her memories, Homura forces herself to complete the witch transformation at the cost of having her soul destroyed, to protect Madoka from the incubators. However, when Madoka appeared, she had forgotten about her duty as the Law of Cycles and her power as such, thus Kyubey kept observing her until that point. As Homura realizes that said witch must be no other than herself, Kyubey appears and reveals that she had fallen into despair and when she was about to become a witch, he and the other incubators isolated her soul gem to set a trap for Madoka, in order to take control of the Law of Cycles.

However, Homura realizes something is amiss and after some investigation recovers her lost memories and realizes that she, Madoka, the other girls and several of their friends are trapped into an alternate world inside a witch's barrier. Madoka and the other magical girls reappear at Mitakihara fighting some new creatures born from humans' negative feelings known as 'Nightmares' (ナイトメア Naitomea?), having no recollection about what previously happened.

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