Every day, Aya Asagiri contemplates suicide. She faces relentless bullying at school, and at home, her older brother Kaname physically abuses her to vent the academic pressure their father places on him.
One night, while lying awake wishing for death, a mysterious website named Magical Girl Site appears on her laptop, offering to grant her magical powers. Initially, she dismisses it as a creepy prank, but when she discovers a magical gun in her shoe locker the next day, she is uncertain what to believe. Deciding to take it with her, she soon encounters her bullies again. This time, desperate for anything to rescue her, she uses the gun—and her attackers are teleported to a nearby railroad crossing, where they are struck by a train.
Aya's conscience cannot bear the fact that she killed two of her classmates with magic, and she frantically tries to make sense of the situation. However, when she finds herself in danger once more, she is rescued by Tsuyuno Yatsumura, a classmate who can stop time using magic. This duo has much to accomplish: not only must they fight alongside and against other magical girls, but they also need to uncover the truth behind the website and the impending apocalyptic event known as "The Tempest."