Nanoha and Yūno say their farewells to the TSAB and they both head home.

When Takamachi Nanoha, a 3rd grader elementary school girl, finds a wounded ferret and takes care of it she finds out she has magical powers and helps it fight a monster that attacked it.

Nanoha is ambushed by Vita for her Linker Core.

On the magical world of Midchilda, Vivio Takamachi is a 10-year-old girl who lives with her adoptive parents, Nanoha Takamachi and Fate T. Harlown, and goes to school with her friends Corona Timil and Rio Wesley. To celebrate Vivio entering her fourth year of elementary school, Nanoha decides to give her her own rabbit-shaped Intelligent Device, which she decides to name "Sacred Heart" or "Chris" for short. Using her new device, Vivio transforms into her mage form, taking the adult Sankt Kaiser form she previously used during an incident several years ago, which comes as a surprise to Fate. As Vivio does some late night training with Nanoha, her Strike Arts instructor, Nove Nakajima, hears about a girl going under the name of the Sankt Kaiser Heidi E. S. Ingvalt who has been attacking various people. The next day, after Nove accompanies Vivio to visit her comatose friend, Ixpellia, she is challenged by the self-proclaimed Ingvalt.

After Nanoha transformed into a magical girl she and Yuuno fight the Jewel Seed and win. Yuuno tells Nanoha about him, the Jewel Seeds and her new magical powers when a new Jewel Seed appears and they go fight it.

Nanoha is exhausted from living her life as a normal girl during the day, and her magical girl life at night, but she has managed to get five Jewel Seeds. When a boy on her father's soccer team activates a Jewel Seed, it is up to Nanoha to save the town.

Suzaka invites Nanoha and Arisa over for a tea party. However, it is interupted for Nanoha when a jewel seed is activated. A mysterious black mage girl comes to claim the Jewel Seed, is she friend or foe?

Fate and her familiar Arf challenge Nanoha at a hot spring.

Arisa suspects that Nanoha is hiding something.

Fate's mother, the real villain, is revealed just as the Time-Space Administration Bureau arrives.

Nanoha joins with the Time-Space Administration Bureau. Yūno reveals his human form to Nanoha.

Nanoha ignores orders and tries to help Fate.

Arf is thrown out by Precia and joins Nanoha. Nanoha visits her friends and family, and sorts everything out.

Nanoha and Fate battle for all the Jewel Seeds, and Fate's origin is revealed.

In the final battle, the TSAB march on the Garden of Time.

Nanoha and Fate fight the much stronger Wolkenritter.

Raising Heart and Bardiche demand a new and dangerous modification to their design.

Hayate's condition worsens, and the TSAB corner the Wolkenritter.

A masked man appears to help the Wolkenritter, whose artificial nature is revealed.

Hayate's love has given the Wolkenritter emotion, and though she says not to hurt anyone, they ignore this in order to protect her.

Fate and Nanoha again confront Signum and Vita, trying to get them to open up.

Nanoha and Fate meet Hayate, and the TSAB realize that the Book of Darkness is going to kill her.

While Chrono researches Graham, the masked man- well, two of him- complete the Book of Darkness at great cost and frame Nanoha and Fate for the crime.

Hayate is engulfed by the Book's power. Chrono confronts Graham on the past and gets a new weapon.

Fate faces her dreams up against reality, while Nanoha battles the Book of Darkness.