The story of Ninku centers on Fuusuke, an odd-looking 12-year-old boy who is a powerful warrior trained in the Ninku school of martial arts, a style that blends ninjutsu and karate. It is explained that prior to the present timeline, those capable of using Ninku were targeted by an evil empire, leading to the formation of the Ninku corps to combat this menace. When the war ended, the Ninku were defeated and nearly all of them were killed because they were deemed useless and dangerous to the rulers. At the start of the story, three years later, Fuusuke, the young former captain of the 1st Ninku corps and controller of the wind, along with Hiroyuki, his flatulent penguin, begin searching for the other Ninku captains, each of whom can control various elements. However, a new group of Ninku users has arisen and is attempting to take over the world. Fuusuke and his penguin must defeat the new Ninku empire with the help of his old comrades.