Yuuno Scraia is a mage from a distant planet working to fix the problem he started when Jewel Seeds were accidentally spread around the world. In a failed attempt to seal a seed properly, he winds up on Earth in the form of a ferret. However, his battle with the seeds did not end upon reaching the Earth and he needs somebody else's help to seal the seeds for him. Takamachi Nanoha hears his telepathic cries for help and comes to his rescue. When she is given a pearl known as the Raging Heart she is able to transform into Magical Girl Lyrical Nanoha and wield a staff to fend off the evil that lies within the Seeds. In order to help Yuuno complete his mission, she needs to seal all 21 Jewel Seeds away, but Fate may be playing a hand in the matter to prevent Nanoha's goals.
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.
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 Yūno say their farewells to the TSAB and they both head home.