Invisible to humans, "wraiths" are beings that feed on human emotions and cause chaos wherever they go. Magical girls must use the power they have gained in exchange for having one wish granted to protect humans from these wraiths. A group of magical girls in Mitakihara have been giving their all to keep the town safe, but two of their members, Sayaka Miki and Kyouko Sakura, can't seem to get along. Their leader, Mami Tomoe, hopes that they can work together in time, but worries that their quarrels will begin to affect their magical girl duties.

Joining this group of magical girls is Homura Akemi, who has recently transferred to Mitakihara Middle School. But Homura knows more about magical girls than she lets on, as well as the truth behind the current state of their world.