Fey, the beautiful and innocent daughter of a wealthy land owner, made friends with her maid Sophia and her friend John. But when she was sent to a school she left John in the care of Sophia, now she's finally back, and it seems to be the end of her innocent days.

Haruki spends most of his time with friends and fellow classmates Airi and Ayana. All seems well, that is until Airi and Ayana form separate clubs, the Mechanical Science Club and the Chemical Science Club. The two vie for Haruki's attention and hilarious chaos usually follows all attempts to make him join.

Six months after the events of Magical Girl Lyrical Nanoha: The Movie 1st, Fate has returned to Uminari City with Lindy as her legal guardian and is living the life of a normal elementary schoolgirl along with Nanoha and her friends. The reunion between the two new-found friends is cut short, however, when they are assaulted by four ancient magic users who identify themselves as the Wolkenritter. As the motives behind the actions of the Wolkenritter become clear, Nanoha and Fate find themselves in a race against time to stop the reactivation of a highly dangerous artifact known as the Book of Darkness.

In 2007, the inhabitants of Danger Planet II fight their battles using remote-controlled robots or "virtual puppets." Kirio Nimura is a high school student and the strongest puppeteer on the planet, until he falls for Sairi Takahara, who insists that nobody may make advances until they have beaten her puppet, Benkei.