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 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...

For summer break, Ittoki returns to the Iga village. Kirei and Ryoko wind up staying in Iga as well, and everyone has a nice time together. Ittoki gets to experience the warmth of the people of Iga. All the while, Kirei is sending Suzaku intel on Iga...

Suddenly, ninja leaders from all across Japan are summoned to a Ninja Grand Council. Yumika, Tokisada, and Kozo attend. Koga's Acting Chief also appears. Then, Goshogawara, head of the NSC, reveals the purpose of the Grand Council...

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.

Koga attacks Iga village. Koga deploys a massive number of Asura, mechanical ninjas, in an attempt to force Iga into submission by overwhelming force. Against the ropes, Ittoki forms a plan to reverse Iga's fortunes.

Kidou's aggressions extend beyond Iga. As chief, Ittoki must bring Iga village together, leaving no time to be lost in sorrow. And is Kousetsu really a traitor? Tokisada's investigation reveals a shocking fact.

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.