Utterly normal middle school student Ittoki Sakuraba is fed up with having to take lessons every day and being monitored by childhood friend Kousatsu. Then one day, a beautiful girl named Tsubaki confesses feelings for him.

Ittoki has suudenly been urged to be come a ninja. After a talk with Tokisada, a ninja feared as the "Demi-god," Ittoki reluctantly agrees. But to get inito the Ninja Academy, Ittoki has to pass the transfer admission exam.

Ittoki decides to give the secret Ninja Core to Kidou. The Iga ninjas oppose it as a declaration of defeat. Kirei, Ryoko, and Suzaku find new resolve. Meanwhile, Iga's traitor is making moves.

Ittoki heads off to settle scores with Onimichi and Onimichi sends all his forces to Iga to exterminate the Iga villages. The final battle of the Shinobi begins.