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In the Rebellion film, we see Homura turn into what she realises is a witch (after she discovers some oddities about the version of Mitakihara city she's supposedly living in) because of her despair.

This reason for her turning into a witch makes sense to me because it would be "valid" under the laws of the universe prior to Madoka's changing of them. However, I'm a bit confused about how Homura managed to become a witch after the law of cycles came into "effect", if under this regime, magical girls disappear instead of becoming witches once their energy is used up.

Why exactly then was there this "exception" to the law of cycles? (I might have missed something since I haven't really followed Puella Magi Madoka Magica very closely.) I suppose the fact that Homura is the only person around who knows of what the former "regime" was might be important in this, but I think I probably missed something when I watched the film.

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From the wiki page this should be the part:

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 her power. However, when Madoka appeared, she had forgotten about her duty as the Law of Cycle and her power as such, thus Kyubey kept observing her until that point.

My guess would be: the Incubators trapped the soul of Homura before the occurence of the Law of cycles i.e. moments before becoming a witch (which is also confirmed by the incubators at a certain point when they say that Homura is between the two states), and it shouldn't contradict the law of cycles because after all it's Madoka who stops the magical girls from turning into witches.

She decides then to become a witch in order to destroy her own soul, so that Madoka won't be trapped by the Incubators, who wanted to study her so that they would have been able to restore the old (magical girl->witch) rule. After all, Homura's soul was kept there for that reason (I previously wrote "her" but it was ambiguous).

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