风助是一个样貌古怪（长得有点像哈巴狗）、个头矮小、食量惊人的小男孩,但其实是极其强悍的忍者。当时世界刚退出了战争, 战乱时决定天下的最后一战, 由忍空组得胜。可惜在和平安后, 当时的忍空组英雄, 郄沦为恶势力的组织, 在社会上无恶不作。风助途经的地方, 都发觉市民受着忍空组的欺压, 为了他们, 风助决意表露自己的身份, 决定独自对抗忍空组,原来他竟是……

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。

The story in Ninku is about an odd-looking 12-year-old named Fūsuke (Fūsuke of the wind) 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 (Eto) and each captain of the corps was called the zodiac animal Ninku master (Etonin). When the war was over, the Ninku were defeated and almost all of them were killed since they were useless and were also dangerous for the rulers. At the beginning of the story, three years later, Fūsuke, the young former captain of the 1st Ninku corps and controller of the wind and Hiroyuki, his flatulent penguin, start searching for the other Ninku captains...

Na guerra, um grupo de guerreiros chamado Ninku lutaram contra o Exército Imperial e quase os aniquilou. Mas no final, o Ninku perdeu e foi fragmentado. Após a guerra, o exército imperial estabeleceu-se como o defensor do povo com a ajuda da propaganda. Eles também conseguiram fazer as pessoas acreditarem que os Ninku foram os vilões que começaram a guerra. Fusuke parece uma criança, mas é o ex-capitão da primeira divisão Ninku. Sua mãe foi levada durante a guerra e depois que os Ninku foram derrotados, e sai em uma jornada para encontrá-la onde encontra Aicho e Touji, ambos também ex-capitães Ninku e, juntos, lutam contra o exército imperial que tenta matar os Ninkus restantes.