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.

Wolkenritter, Nanoha, Fate, Hayate and TSAB alike team up against the final enemy.

Although the danger is averted, the threat to Hayate's life remains. In view of this, Reinforce makes a fateful choice.

Subaru Nakajima and Teana Lanster are taking a test to increase their rank from C to B. During the test, Nanoha, Fate, Hayate, and Rein observe their progress. Near the end of the test, Teana injures her ankle, but Subaru has a plan to complete the test in time.

Subaru and Teana are informed that they have failed their promotion exam, but are given another chance by Nanoha and Reinforce to take the exam again in a week. In the meantime, they are told about the Sixth Mobile Division, which is a special division about to be formed and led by Nanoha, Fate, and Hayate. Erio and Caro make an appearance and meet for the first time.