The anime takes place in a world that long ago featured the existence of magic, but has long since lost that ability. The story begins when the very normal high school student Mangetsu Kohinata meets Shingetsu Ernesta Fukami, who has migrated back to Japan from Germany, on a night with a full moon.

Bell Cranell is a rookie adventurer and the sole member of his dirt-poor guild founded by the petite goddess Hestia. Adventurers come from far and wide looking to strike it big in the massive labyrinth known as Dungeon, located beneath the city of Orario. Bell is more interested in picking up girls than Dungeon-crawling, but his reality check comes sooner than expected. Saved from a brush with death by the beautiful, renowned adventurer Aiz Wallenstein, Bell falls head-over-heels and sets his sights on winning her heart, but she’s not the only woman he’s caught the attention of, for better of worse.

The city is infested with mysterious parasites that bore into their human hosts to increase their host’s power and sexual desires. A beautiful girl, Suzune Arizono is a vet with a specialty in parasites, and who fights daily to end the plague. Before long, she learns that an evil organization, the Kito Zaibatsu, is behind the explosive growth of this ferocious parasite. She also learns that her long-missing father, Dr. Arizono, is also involved. In order to crush the Kito Zaibatsu’s ambition and to see her father again, Suzune takes on the fight without regard to the danger involved.

Set within a city where parasites rage, the parasites settled into their human hosts and increases their power and sexual desires. Dr. Suzune is a parasite expert who works daily to kill the parasites. A sinister demon organization exists behind the parasites. Dr. Suzune also realizes that her father, who went missing when she was a young child, is somehow connected with the group. Violence and madness awaits for her …

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.