After the Book of Darkness incident, Nanoha, Fate and Hayate postpone sending Reinforce away to ensure that the Book's regeneration program won't harm anyone again. However, this means that the remnant pages of the Book of Darkness soon regenerate and Nanoha and her friends are forced to fight them. These remnants take form of twisted, dark copies of the trio called the Dark Materials.

All of the playable characters except the Materials have their own different story route in the game. Every route has the same basic structure: the player must first pass a training session, then defeat the dark clones of two of their best friends, defeat one Material boss, defeat the clones of two more friends, then lastly defeat a Material boss version of themselves.