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 arrives at the Ninja Academy. Meeting the kind and chipper Kirei and the beautiful and graceful Ryoko gives Ittoki hope about life at the Academy, but the Koga students' influence threatens to make life miserable.

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.