The story follows Rantarō Inadera, a boy from a long line of low-ranking ninjas who enrolls at the Ninjutsu Academy, a specialized school hidden in the mountains of the Kinki region, to fulfill his dream of becoming a first-rate elite ninja. The setting is the late Muromachi period, a time of warring states, though the manga freely incorporates modern anachronisms like vending machines and wristwatches for comedic effect. Rantarō quickly befriends his roommates: the orphaned Kirimaru Settsuno, who is obsessed with earning money through various part-time jobs, and Shinbei Fukutomi, the slow-moving, gluttonous son of a wealthy merchant who possesses hidden strength and a powerful head. Together with the rest of the academically struggling first-year Ha class, these three friends constantly find themselves scoring failing grades, requiring remedial lessons, and causing trouble for their long-suffering teachers, the young instructor Doi Hansuke and the practical skills master Yamada Denzo.

The narrative consists of self-contained comedic episodes and longer arcs where the students apply their developing ninja skills to real-world situations. A recurring source of conflict is the Dokutake Castle, a warmongering enemy domain led by its eccentric ninja corps commander, Hieta Hopposai, whose schemes are routinely thwarted by the academy's students. The first volume introduces the trio as they perform duties like dinner service, deliver a secret letter while battling bandits, and undertake a dangerous rescue mission to save Shinbei from the soldiers of Kumonosu Castle. In a notable early arc, Rantarō and his friends befriend Hyōgo Daisankyōeimaru, the seasick and swimming-phobic admiral of the Hyōgo Navy, and help him recover a new type of cannon stolen by the Dokutake ninja, successfully destroying both the weapon and the enemy fort in the process. Another story involves the trio delivering a truce letter between the Enoki and Nameko castles, which leads to further conflicts with enemy forces. The manga is characterized by its blend of historical research and absurdist humor, teaching authentic ninja techniques from historical manuals while simultaneously breaking the fourth wall, with characters climbing out of panel borders or interacting directly with the author.