Months have passed since the Jewel Seed incident, and Nanoha Takamachi is preparing to welcome Fate Testarossa back from her Administrative Bureau trial. Having earned conditional amnesty for averting the crisis, Fate is now allowed to attend school with Nanoha. Yet before the two girls can resume normal life together, a band of shadow mages suddenly attacks them. Overwhelmed by these unknown foes, Nanoha and Fate have their mana siphoned into a foreboding grimoire, leaving Raising Heart and Bardiche damaged.
The attackers are identified as the Wolkenritter; its four members—Vita, Signum, Shamal, and the familiar Zafila—were summoned by the Book of Darkness to carry out its sinister will. The book is presently possessed by the young Hayate Yagami, who remains unaware of its true nature. While the Wolkenritter channels stolen mana to fulfill its duty, it seeks to complete the tome.
Depleted and defenseless, Nanoha and Fate must race against time to regain power and confront the Wolkenritter, aiming to stop the quartet from finishing the Book of Darkness and unleashing its catastrophic magic upon the world.