Fourteen-year-old Madoka Kaname has a surreal dream about a strange creature and a girl in trouble. The next morning, a mysterious girl named Homura Akemi transfers into Madoka's class; to her surprise, Homura appears to be the exact same girl that she saw in her dream.

Later that day, Madoka hears a plea for help in her head. It turns out that the cries belong to an injured Kyuubey, the cat-like creature who was also in her dream. But she finds Homura at Kyuubey's location, who warns Madoka to get away from the small entity. Making the connection that her new classmate attacked the helpless creature, Madoka takes Kyuubey and runs away with the help of best friend Sayaka Miki.

After their escape, Kyuubey offers the girls an enticing opportunity: become a magical girl in exchange for having any wish granted. However, not everything is as it seems, as the weight of their wishes may be a lot heavier than they might have expected.