Madoka makes the decision to become a Puella Magi, wishing to stop all witches from the past, present and future, to erase them before they are born by her own hand, a wish made possible due to the massive power inside her. As she makes the transformation, her conscious is greeted by Mami and Ky?ko. Becoming a god-like Puella Magi, Madoka spreads herself across space and time, absorbing the misfortune from other Puella Magi to prevent them from becoming witches. The gigantic Soul Gem produced cracks into a giant mass of despair, but Madoka's hope manages to quell it. As a result, Madoka becomes an omniscient being, of which there is no evidence of having existed on Earth. Madoka then says her goodbyes to Homura, leaving her with her ribbons so that she won't forget her, before fading from existence, where she joins Sayaka. Homura returns to a world where Madoka doesn't exist, and she, Mami and Ky?ko are fighting together, though Homura still retains her memories of Madoka. With a different type of enemy that are born from curses, Homura continues to protect the world that Madoka loved.
-Wikipedia
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