Beginning in April 1614 Japan, the story centers around the Kouga and the Iga, two rival ninja clans who have been enemies for 400 years.

Danjou and Ogen, leader of the Kouga and Iga respectively, are summoned to Sunpu Castle and each select nine other members of their clan to participate in a battle to the death.

Due to years of incestuous selective breeding, the members of the Kouga and Iga have all developed inhuman abilities at the cost of several of them being born physically disfigured or otherwise abnormally mutated.

At the center of the conflict is Kouga and Iga's two young heirs; Gennosuke and Oboro respectively; who had fallen in love in the hopes of not only bringing their clans together in peace but also to mix the bloodlines of their families so as to undo the genetic damage endured by both.

The novel traces the course of the conflict as both clans endure heavy losses and ultimately bring Gennosuke and Oboro to face each other on the field of battle.