One day, ordinary high school student Kogami Kii finds himself caught up in a strange kind of zombie apocalypse, involving 'magic girls.' While idly looking out of the school window, Kii sees what looks like a little girl hitting a teacher, causing his head to explode violently. Convinced he's dreaming, he goes to the restroom to get his act together.

Unfortunately, its not a dream, and he arrives to find the creepy little girl repeatedly saying "magical" as she slaughters his friends and classmates. Soon, Kii and his childhood friend—a quiet, often-bullied girl called Tsukune—are witness to the resurrection of their friends' corpses into a zombie-like murderous mob crying the single word "magical." Now Kii and Tsukune must try to endure with the other survivors, and try to find out what has happened to their world.