After the Jewel Seed incident, Nanoha Takamachi awaits Fate Testarossa's return from her trial. Fate, granted clemency, joins Nanoha at school. However, their peace is shattered by dark mages who drain their powers and damage their magical devices. The Wolkenritter, led by Hayate Yagami, serve the ominous Book of Darkness, seeking its completion. Now powerless, Nanoha and Fate must recover and stop the Wolkenritter from unleashing chaos with the book's destructive magic.