The film's story is set in the Doll Kingdom where dolls reside. Happiness Charge PreCure are asked to help by a women named Tsumugi when the sudden appearance of Saiarks begin wrecking havoc upon the Kingdom. However all is not what it seems with the mysterious man Black Fang dwelling in the shadows.

Kurotori Chiyoko, a 5th-grader in elementary school, loves the occult. One day, a friend requests her to do a love fortune-telling. Chiyoko tries to summon Cupid, but thanks to a stuffy nose, accidentally summons a witch named Gyubid instead! From that day on, Chiyoko starts learning witchcraft from Gyubid, the self-proclaimed hottest instructor of the magic world. The training regimen is tough, and punishment for slacking is harsh. Fortunately, Chiyoko is able to keep her extra-curricular studies secret, aided by the fact that no one else can see Gyubid.

Saito Hiraga and Louise Françoise Le Blanc de La Vallière go on the offensive after the events of Zero no Tsukaima: Princesses no Rondo. Together, they face off against King Joseph in the Holy City of Romalia with the help of two others who control the power of the “void”. But in the midst of the many conflicts ahead of them, an ancient evil begins to stir in the shadows. Will their close bonds blossom into something more or will they be shattered through the ever increasing difficulty of the tasks that they must undertake? Zero no Tsukaima F follows the story of Louise and Saito as they face their final challenges together.

Five dangerous "seeds" have been stolen from their vault in the world of Evergreen and taken to Earth. Natsuki, an agent of the Queen, has been sent to retrieve them. However, he cannot do this alone and enlists the aid of Chihaya, a middle school student, who is "the only one" who can help him. With his aid she transforms into Magical Warrior Carmine in order to save the humans possessed by the seeds. Questions abound though, such as why Chihaya's mother appears to know all about this secret activity, why Chihaya remembers her father who reportedly died before her birth, and why she dreams of Evergreen, which she has never seen.