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.

Six months after the events of Magical Girl Lyrical Nanoha: The Movie 1st, Fate has returned to Uminari City with Lindy as her legal guardian and is living the life of a normal elementary schoolgirl along with Nanoha and her friends. The reunion between the two new-found friends is cut short, however, when they are assaulted by four ancient magic users who identify themselves as the Wolkenritter. As the motives behind the actions of the Wolkenritter become clear, Nanoha and Fate find themselves in a race against time to stop the reactivation of a highly dangerous artifact known as the Book of Darkness.

"Fuyu no Chikai, Natsu no Matsuri - Takeoshi no Dai-Kusunoki" is set in the city of Takeoshi, and will center on two characters, a boy and a girl, who grow up watched over by a large camphor tree that endures the time and seasons. It will star Nao Tōyama as Rinko Yamaguchi, and Nobunaga Shimazaki as Sōta.

"Yakusoku no Utsuwa - Arita no Hatsukoi" will be set in the town of Arita, and will be a youth story highlighting the scenery of Arita. It will star Hiro Shimono in the role of Jun Uchiyama, and Saori Hayami in the role of Nao Akiyama.