The film’s story begins when Arata inadvertently touches “Hermes Apocrypha,” Lilith’s Grimoire. Suddenly, he is enveloped by a bright white light, and a girl appears before him. She calls herself Lilim, and treats both Arata and Lilith as her parents. At the same time she appears, something changes in the world. The forbidden Eternal Library awakens. In the Library is sealed the ultimate culmination of Alchemy, the White Demon Lord. The White Demon Lord plots to eliminate Arata and the Trinity Seven to usurp the position of Demon Lord. Bristling with untold power, the White Demon Lord attacks Arata, and triggers a desperate crisis where Arata and the Trinity Seven must save the world in this last battle.

The story of the film begins after the events of the second season, at the graduation ceremony of the third-year students. Knowing that the graduation of the third-year members means the end of μ’s, the nine girls take a walk around the school filled with memories. However, when the students attempt to leave the school gates, a single email is sent to them, and the curtain on a new story for μ’s begins.