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.