The story in Ninku is about an odd-looking 12-year-old boy named Fuusuke (Fuusuke the wind (&#39080;&#12398;&#39080;&#21161;, Kaze no F&#363;suke?)) 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 (&#24178;&#25903; Eto) and each captain of the corps was called the zodiac animal Ninku master (&#24178;&#25903;&#24525; 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 (&#12498;&#12525;&#12518;&#12461;), 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. 
--wikipedia

In the war, a group of warriors called Ninku fought against the Imperial Army and almost annihilated it. But in the end, the Ninku lost and got shattered. After the war, the imperial army established themselves as the defender of the people with the help of propaganda. They also managed to get the people to think the Ninku were the villains and had started the war. Fusuke looks like a child but he is the former captain of the first Ninku division. His mother was taken during the war and after the Ninku were defeated, he goes on a journey to find her. On his journey he meets Aicho and Touji, both also former Ninku captains, and together they fight against the imperial army that tries to kill the last remaining Ninkus. 
The ninku is a clan of extinct ninjas who command esoteric and powerful techniques, hence a lot of other groups are constantly trying to steal their techniques to take over the country. Their primary target is Fusuke, a weird looking kid but one of the most powerful Ninku ninja. Fusuke, together with other Ninku ninja with different specialties must fight those threat that caused the downfall of the Ninku clan.
 
(Source: Anime News Network)

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