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.

The movie centers on Rantaro's teacher Hansuke Doi losing a battle against Sonnamon and Zatto Konnamon becoming a teacher at Ninjutsu Academy.

Some unknown castle hire Yamada Rikichi to steal back the secret medicine which was stolen by Dokutake Castle. On the other side, Dokutaka attack and took Fukutomi Shinbei and Kato Danzo’s carrying. Danzou went chasing Dokutake Ninja, while Shinbei run and report the incident to Ninjutsu Academy. And first year ha class went to rescue Danzou after hearing the message.