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. At the same time, Ninjutsu Academy receives a request for support from a village troubled by the war, and Rantarou and the remaining students and teachers head there to help out.

The movie is an alternate retelling of content from the manga that was already adapted in season 16 of the anime, with completely new animation, events in a different order and added new material.