Takamachi Nanoha is a normal third-grader who feels a little useless and out-of-place with no purpose. Then one day, she saves a ferret, who turns out to be a mage from another planet who came to this planet to search for the jewel seeds. Nanoha agrees to help, but this task gets complicated when another girl arrives to steal them.

The planet Eltria, having suffered severe desertification in the past, has all but been abandoned. Against her older sister's wishes, Kyrie Florian travels to Earth alongside her best friend, the AI Iris, in search of the key to their planet's regeneration. However, the only way to find it lies within the Tome of the Night Sky, leading them into conflict with Nanoha and her friends.

As the conflict that began in Magical Girl Lyrical Nanoha: Reflection continues to escalate, Nanoha and her allies soon find out the troubled history between Iris and Yuri, which is related to the tragedy of Eltoria's "Planet Reclamation Committee".

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.