The story unfolds during a sweltering summer break at a ninjutsu academy in a war-torn version of historical Japan. The young students of the first-year Ha class, the energetic and good-hearted Rantaro, the money-loving and shrewd Kirimaru, and the strong but simple-minded Shinbei, have spent their entire vacation playing by the river without a single thought for their looming summer homework assignments. Just as panic sets in over their unfinished work, a crisis erupts. A legendary blade known as the Gokurakumaru, or Heaven s Sword, which is said to grant its wielder the power to conquer the world, is stolen from the master swordsmith Rokusai Tsujikando. The thief is Kirara Takaoru of the木耳 Castle, who quickly delivers the sword to the nefarious Hieda Hachizosai, the leader of the rival Dokutake ninja clan, who plans to use its power to destroy the Ninjutsu Academy.

Seeing an opportunity for both education and defense, the eccentric Headmaster tasks Rantaro, Kirimaru, and Shinbei with infiltrating Dokutake Castle and retrieving the stolen sword. As an irresistible incentive, he promises that if they succeed in this dangerous mission, they will receive all the answers to their summer homework. Joined by their strict but caring teacher, Doi Hansuke, and the skilled upperclassman Takamaru, the three young ninja embark on their first real mission. Their journey is filled with comical traps, fierce rival ninjas, and the realization that they are not the only ones seeking the blade, as other clans and rogue operatives maneuver for power.

The narrative arc follows the trio from a state of childish panic over schoolwork to a genuine test of their skills and courage. They must navigate the treacherous defenses of Dokutake Castle, only to discover that the sword they recover is a fake, deepening the mystery. The mission forces them to rely on their unique and often unorthodox abilities. While the fate of the academy and potentially the nation hangs in the balance, the personal goal of passing their summer class remains an equally urgent and charming motivation for the young protagonists. The climax sees them confronting Hachizosai and his forces in a final, chaotic battle to secure the real Gokurakumaru and save their school from destruction.