Complex sentence: Afterwards Homura captures Kyubey and rewrites the laws of the universe once again to create a new world where Madoka can live in peace, but at the end she realizes that Madoka will eventually remember the truth and when that happens, they might become enemies.
Split into simpler sentences: Afterwards Homura captures Kyubey and rewrites the laws of the universe once again to create a new world where Madoka can live in peace. At the end, however, she realizes that Madoka will eventually remember the truth and when that happens they might become enemies.