The movie picks up after the events of the original television series, where Madoka became a god-like entity and restructured the universe to prevent magical girls from becoming witches. Homura, who was once Madoka's best friend and ally, is now left alone and bitter as she is the only one who remembers the original timeline where Madoka sacrificed herself to save everyone.
Despite the new arrangement of the universe, Homura discovers that the magical girl system is still corrupt and flawed. The young girls who become magical girls still suffer, and the system still demands their lives as a price for their wishes. In addition to this, Homura discovers that her memories have been tampered with and that she is not who she thought she was.
As Homura fights her way through the nightmares that continue to haunt the magical girl system, she comes face-to-face with a new enemy. This enemy forces her to take drastic measures to save Madoka and herself, leading to an epic battle that will determine the fate of the universe once again.
Ultimately, the movie focuses on Homura's feelings of isolation and her struggle to understand Madoka's new existence as a god. The ending is controversial and open to interpretation, leaving viewers to question whether Homura's actions were justified or if they were merely the result of her own selfish desires.