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The Dokutake ninja steal a shipment of saltpeter from Shinbei's papa. They plan to use it to create medicine that will make them fly and become super-ninjas! Danzou, who's father was transporting the goods, stows away and is taken to the Dokutake's secret headquarters. When Shinbei informs the school, Yamada-sensei and Doi-sensei rush to help. But Hagumi decide to take matters into their own hands and try to rescue Danzou themselves. Things don't go according to plan, though, and soon they all need to be rescued too. Fortunately Rikichi, Yamada-sensei's cool son, is around to help out! In fact,before long everyone gets into the act! But can Rantarou and his friends stop Happousai before it's too late?
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 Ninjutsu Academy, Doi teaches young ninjas known as "Nintama." One day, he goes out for a battle against a ninja from the rival clan, but vanishes without a trace. The Nintamas worry for Doi's safety. At the same time, the Academy receives troubling news that their rivals at Dokutake Castle may be scheming something.