Rantarō, Shinbei and Kirimaru are ninja apprentices in the Ninja Gakuen, where first grade ones are called "Nintamas". They must learn everything a ninja must know, but as for our heroes, money, food or playing are more interesting. The series show the everyday adventures of our heroes.

Six months ago, Hikaru vanished for a week. Now, as his best friend Yoshiki senses something amiss and confronts him, the harrowing truth emerges.

Love is unusual for Koizumi Risa and Ootani Atsushi, who are both striving to find their ideal partner in high school—172 cm tall Koizumi is much taller than the average girl, and Ootani is much shorter than the average guy at 156 cm.

The Ninjutsu Academy students return from summer break to hear that due to one of Komatsuda's mistakes, all their summer homework was mixed up. As a result Kisanta, who received an assignment meant for a sixth year, has gone missing after trying to sneak into Oomagatoki Castle to steal their lord's fundoshi. A group including Shinbei and Kirimaru is sent to rescue him, but since Oomagatoki is at war with Tasogaredoki Castle it might be a difficult mission.