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.

In the future, the moon is a habitable place with atmosphere and gravity and also a famous tourist attraction. There are also stories about a "long ears" creature like rabbits on the moon who can use magic. Haruka Daichi heads off to the moon during a summer holiday alone because he likes to see the long ears creature by himself. However, he get himself dragged into an ancient conflict between two ancient moon races: the "long ears" race and Jado race. Jado race wanted to conquer the universe and resurrect ancient evil powers to seize control of the Earth. Now the "long ears" race and Daichi must seek three warriors who could use magic to release Mado King to fight Jado race and to release "long ears" race's kingdom, Rabiluna, from Jado race.

Asta and Yuno were abandoned at the same church on the same day. Raised together as children, they came to know of the "Wizard King"—a title given to the strongest mage in the kingdom—and promised that they would compete against each other for the position of the next Wizard King. However, as they grew up, the stark difference between them became evident. While Yuno is able to wield magic with amazing power and control, Asta cannot use magic at all and desperately tries to awaken his powers by training physically. When they reach the age of 15, Yuno is bestowed a spectacular Grimoire with a four-leaf clover, while Asta receives nothing. However, soon after, Yuno is attacked by a person named Lebuty, whose main purpose is to obtain Yuno's Grimoire. Asta tries to fight Lebuty, but he is outmatched. Though without hope and on the brink of defeat, he finds the strength to continue when he hears Yuno's voice. Unleashing his inner emotions in a rage, Asta receives a five-leaf clover Grimoire, a "Black Clover" giving him enough power to defeat Lebuty. A few days later, the two friends head out into the world, both seeking the same goal—to become the Wizard King! [Written by MAL Rewrite]