Nanoha Takamachi, an ordinary third-grader who enjoys spending time with her family and friends, rescues an injured ferret that she had dreamed about the night before. The next day, the ferret cries out to her telepathically, asking Nanoha to save him. The ferret reveals himself to be Yuuno Scrya, a mage from another world who is trying to collect the dangerous 21 Jewel Seeds that he accidentally scattered across the world. He enlists Nanoha's help, gifting her the magical wand Raising Heart, and teaches her how to become a powerful mage.

Days later, after reclaiming a few of the Jewel Seeds, another mage appears: Fate Testarossa. Stronger than Nanoha, Fate refuses to divulge her reasons in trying to collect the Jewel Seeds. Nanoha senses a melancholy in her eyes, but Fate refuses to communicate. Directed by Akiyuki Shinbo, Mahou Shoujo Lyrical Nanoha is a story about the clash of emotions when goals collide.