A girl with nothing becomes the flashpoint for a war that should never happen. Kamijou's powerlessness against the machinery of two worlds, magic and science both grinding toward collision, forces him to fight with his fists and his refusal to let Arisa become a tool. The movie trades the TV series' episodic sprawl for a single, escalating nightmare where every decision narrows the path forward instead of opening it.

Academy City stands on the brink of completing its most ambitious project yet: Endymion, the world's first space elevator. Before it is finished, Kamijou and Index meet and befriend Arisa Meigo, a cheerful, ambitious singer who is a Level 0. Magicians attack the city in pursuit of her, and a unit led by a woman named Shattoaura moves to fight them off. As strange events spread across the city, an intricate plot surrounding Arisa and Endymion comes to light. When Stiyl appears, Kamijou and Index learn from him that Arisa is central to a looming war between the sides of magic and science. The film is a science fiction action story with a strong musical thread.