Several months have passed since the Jewel Seed incident, and Nanoha Takamachi is getting ready to welcome Fate Testarossa back from her trial with the Administrative Bureau. Having received conditional clemency for her role in preventing the crisis, Fate has been allowed to attend school with Nanoha. However, before the two girls can settle into their daily lives together, a group of dark mages suddenly descend upon them. Overpowered by their unknown assailants, Nanoha and Fate have their mana absorbed by an ominous grimoire, and both Raising Heart and Bardiche are damaged in the process.

The ones behind this ambush are known as the Wolkenritter, and its four members—Vita, Signum, Shamal, and the familiar Zafila—were summoned by the Book of Darkness to carry out its malignant bidding. The book's current owner is the young girl Hayate Yagami, oblivious to its true nature while the Wolkenritter, charging its power with the forcibly stolen mana, is duty-bound to seek the tome's completion.

Left drained and weaponless, Nanoha and Fate must race against time to recover their strength and confront the Wolkenritter, with the aim of preventing the quartet from finishing the Book of Darkness and unleashing its devastating magic upon the world.