Kazama Endo is an undefeated high-school delinquent who lives for nothing but fighting the strongest opponents he can find. When two of his underlings are beaten by a boy named Ichiya Hachisuka, Endo tracks him down, ready for a brawl. To his surprise, Hachisuka is no ordinary street fighter—he is a ninja. Their clash ends in mutual respect, and the two quickly bond over their shared obsession with strength. Together, they set their sights on the pinnacle of the hidden ninja world: the title of Oniwaban, the elite guardians of the ninja realm.

To pursue this goal, Endo transfers to Jinshin High School, a battleground where three rival ninja factions—the Iga, the Koga, and the unaffiliated—constantly vie for supremacy. As soon as Endo arrives, word spreads that he carries the blood of the forbidden Fuma clan, a lineage long considered taboo. Each faction immediately tries to recruit him for its own advantage. Endo, however, has no interest in serving anyone. He begins cutting through the school's hierarchy with raw power, quickly attracting a loyal following of strong-willed fighters.

Endo soon crosses paths with Sarutobi Rondoko, a prodigy known as the strongest second-year at Jinshin. Their fight ends in a draw after Endo unleashes his inherited technique, the Fuma Shuriken Fist. Rather than remaining enemies, they become unlikely allies and even share a bowl of ramen together. This alliance draws the ire of the Koga-dominated student council, which begins targeting Endo and his growing circle. In response, Endo forms an informal army known as Team Endo, gathering a crew of formidable ninja outcasts and renegades.

The student council responds by dispatching a ruthless assassin named Seki, who has no qualms about harming innocent bystanders. Seki defeats Hachisuka in a brutal fight, sending him to the hospital. Enraged, Endo confronts the council, and a full-scale war erupts across the school grounds. The battles are fierce and personal: Kirigakure fights Mochizuki to earn the recognition he has craved since childhood; Doshima clashes with Gara in a desperate attempt to live up to his own ideals; and Rondoko faces Tobayashi, whose bloodline technique of gravity manipulation seems nearly unbeatable.

As the conflict escalates, darker forces move behind the scenes. The mysterious Kunisada organizes a Nin-Sen tournament to select a new Oniwaban, but suspicions arise that his true aim is to overthrow the Japanese government. Meanwhile, Gara—while investigating the Fuma clan—inadvertently draws the attention of Fuma Kotaro, the most feared ninja alive and a man whose power dwarfs nearly everyone on the board. At the same time, the secrets of Endo's own lineage begin to surface, and Zankuro, a perceptive observer, starts to piece together the truth about Endo's past. These converging threads push the story toward a collision between the student-council war, the political struggle for control of the ninja world, and the shadow of the Fuma clan's legacy.