The pupils of Ninjutsu Academy returned to school after their summer break only to learn that one of Komatsudas errors had caused all their summer assignments to be mixed up. Kisanta, who received an assignment intended for a sixth-year student, went missing after attempting to sneak into Oomagatoki Castle in order to steal the lord's fundoshi. To rescue him, a group consisting of Shinbei and Kirimaru was dispatched. However, since Oomagatoki is currently at war with Tasogaredoki Castle, this mission may prove challenging. Meanwhile, Ninjutsu Academy received an appeal for assistance from a village that has been affected by the conflict. Rantarou and the remaining students and teachers set out to help resolve the issue.
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.
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