Sorry if I sound stupid, I was just confused with everything happening... How is Madoka not a god at the end of the movie?

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    Rebellion is very confusing. Take a look at our other Madoka questions and notice how many of them are asking "Why did this happen in Rebellion?" – Torisuda Dec 24 '16 at 16:45

Madoka is still a God, albeit maybe broken (i'll explain).

What Homura did was separate Maodka into 2, the God Madoka who is the Law of Cycles and the Human Madoka who existed before attaining her divinity which Homura separated from the Law of Cycles.

these however are both still the one Madoka as near the end (before Homura gives back Madoka's Ribbon) Madoka begins to remember that she was apart of something greater and her eyes change to the same colour as that of her god self. we see that Homura tries to stop Madoka in remembering because if Madoka remembers she'll return to being a God, removed from the world with no one knowing she ever existed.

Why is Madoka broken? Sayaka hints on this when Homura first created the new universe asking if Homura was planning on destroying the universe, this would indicate that the Law of Cycles is broken in some way. we're not sure in what way but given that the Law of Cycles purifies Puella Magi before becoming Witches we can assume that Witches can be born again, the threat on the Universe probably being how Madoka's own witch was capable of doing this so another witch can aswell.

Also if Madoka being able to exist wasn't such a great deal then why is Homura worried about Madoka regaining her memories as the Law of Cycles? this would indicate that in Homura's Universe the Law of Cycles still exists and needs the human Madoka back.

However we don't know the full extent of what Homura's Universe is like. all we know is that Homura had greater control (being able to seal Nagisa's and Sayaka's memories/witch powers), Witches can possible be born, Wraiths still exist and the Incubators are being forced to manage the curses of Earth. we don't know for certain what Sayaka meant by the universe being destroyed or why Madoka can not exists as a human with the memories of having been a god.

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