Upon their return from summer vacation, the students at Ninjutsu Academy were informed of a grave mistake made by Komatsuda. The summer assignments were all mixed up, which caused Kisanta to disappear as he was assigned a task intended for sixth-graders. Kisanta had secretly attempted to steal the lord's fundoshi from Oomagatoki Castle. To ensure his safety, a team including Shinbei and Kirimaru was sent to rescue him. The rescue mission was expected to be quite challenging as Oomagatoki was currently at war with Tasogaredoki Castle. At the same time, the Academy was contacted for assistance by a village struggling with the effects of the war. Rantarou and the rest of the students and faculty decided to help and set out on a mission to aid the distressed town.