In the distant technological future, civilization has reached its ultimate Net-based form. An "infection" in the past caused the automated systems to spiral out of order, resulting in a multi-leveled city structure that replicates itself infinitely in all directions. Now humanity has lost access to the city's controls, and is hunted down and purged by the defense system known as the Safeguard. In a tiny corner of the city, a little enclave known as the Electro-Fishers is facing eventual extinction, trapped between the threat of the Safeguard and dwindling food supplies. A girl named Zuru goes on a journey to find food for her village, only to inadvertently cause doom when an observation tower senses her and summons a Safeguard pack to eliminate the threat. With her companions dead and all escape routes blocked, the only thing that can save her now is the sudden arrival of Killy the Wanderer, on his quest for the Net Terminal Genes, the key to restoring order to the world.
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.
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.
