The story in Ninku is about an odd-looking 12-year-old boy named Fuusuke (Fuusuke of the wind (風の風助, Kaze no Fūsuke?)) who is a powerful warrior from the Ninku school of martial arts, a style that mixes ninjutsu and karate.
It is explained that before the present time in the story that those who could use Ninku were targeted by an evil empire and the Ninku corps were formed to combat the menace. The names of the corps were taken from the twelve Chinese zodiac animals (干支 Eto) and each captain of the corps was called the zodiac animal Ninku master (干支忍 Etonin). When the war was over, the Ninku were defeated and almost all of them were killed (except for a few corps' captains) since they were useless and were also dangerous for the rulers. At the beginning of the story, three years later, Fuusuke, the young former captain of the 1st Ninku corps and controller of the wind and Hiroyuki (ヒロユキ), his flatulent penguin, start searching for the other Ninku captains, each of whom can control various elements. However, a new group of Ninku users has arisen and are trying to take over the world. Fuusuke and his penguin must defeat the new Ninku empire with the help of his old comrades.
「忍空」――それは、空手と忍術を組み合わせた史上最強の武術である。大戦の中、わずかな人数で敵部隊を壊滅に追い込んだ忍空使い集団「忍空隊」は、なぜか突然、戦うことをやめ解散。忽然とその姿を消す。やがて戦争が終わり三年。人々は戦争の恐怖からは解放されたが、新政府の圧政に苦しんでいた――。 元・忍空隊の風助(ふうすけ)は、幼い頃連れ去られた母の消息を求めて旅をしていた。風助はその途中、昔の仲間たちと出会い、彼らとともに旅を続けることになる。
在治理了忍空組所活躍的戰亂之後的江戶曆(EDO暦)3年,風助在旅行途中目擊到忍空組剩下的的餘黨們正在做壞事。在另一方面與風助同於忍空修行的橙次去接應被囚禁的餘黨和激進派們,同時他們自稱為「忍空狼」並把一個接一個讓隊長們顏面無光然後握有一定實力的刺客們從干支忍那邊放出來,就這樣雙方發動了忍空戰爭。