Each day Aya Asagiri contemplates ending her life. At school she endures relentless bullying, and at home her older brother Kaname physically abuses her to cope with the academic pressure imposed by their father. One night, while lying awake and wishing for death, a strange site called Magical Girl Site appears on her laptop, promising to grant her magical abilities. Initially she dismisses it as a creepy joke, but the next day she discovers a mystical gun in her shoe locker and is unsure what to believe. She takes it with her, and when she confronts her bullies again, desperation drives her to use the weapon—sending her attackers to a nearby railroad crossing where they are struck by a train. Aya cannot bear the guilt of killing two classmates with magic, and she scrambles to make sense of her actions. When trouble strikes again, Tsuyuno Yatsumura—a classmate who can halt time—rescues her. Together they must confront other magical girls, investigate the origins of the site, and prepare for the impending apocalyptic event known as The Tempest.