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.

The practical exam is coming up. Since there are fatalities every year, Koga intends to use it as an opportunity to kill Ittoki. Ittoki questions world of ninjas. In preparation for a showdown with Suzaku, Kousetsu and Ittoki form a plan...

Yumika's death sentence brings turmoil to Iga. As Acting Chief, Ittoki's leadership is tested, but he is still in shock over his mother's imprisonment. Meanwhie, in Koga, something fearsome is beginning to move.

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.