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.

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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.

Hayate's dream of this new unit has finally been realized and the training begins for the new recruits. New characters are introduced which gives insight to the new villan's plot of the Lost Logia named Relic.