Brought together by a mysterious song, a grad student and an engineer lead the fight against an unimaginable force that may spell doom for the world.

Kiyotaka Ayanokoji has just enrolled at Tokyo Koudo Ikusei Senior High School, where it's said that 100% of students go on to college or find employment. But he ends up in Class 1-D, which is full of all the school's problem children.

What's more, every month, the school awards students points with a cash value of 100,000 yen, and the classes employ a laissez-faire policy in which talking, sleeping, and even sabotage are permitted during class.

One month later, Ayanokoji, Horikita, and the students of Class D learn the truth of the system in place within their school...

Following Madoka's rewriting of the universe, sacrificing herself and her happy normal days to save all magical girls from the cruel fate that awaited them by wiping witches out of existence, the despair still manifest into creatures known as nightmares. Magical girl Homura Akemi continues to fight alone in the hope that she will be able to see Madoka smile again.