There exist strange creatures who have the power to grant one wish to a chosen girl.
However, in exchange, that girl must then become a Puella Magi, a girl with magical powers, and fight against witches, evil creatures born from darkness that are responsible for murders and suicides.

In the city of Mitakihara, a schoolgirl named Madoka Kaname and her friend Sayaka Miki are approached by a familiar named Kyubey, who offers to grant them each one wish in return for making them Puella Magi.

 Another Puella Magi named Homura Akemi tries to prevent Madoka from making such a deal, while Kyubey urges Madoka by telling her she will become the most powerful Puella Magi.