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Set in the modern age, the story is about Rokujo Miharu, who just wanted to live a normal life and inherit a Okonomiyaki restaurant. At the moment, his biggest problem was the constant pestering from Kouichi Aizawa and Durandal Thobari Kumohira, who started a Nindō (忍道, Nindō? lit. "Way of the Ninja") Club. Miharu wanted nothing to do with "ninjas" and turns them down every time. But soon, he is attacked by an actual group of ninjas and is protected by Kouichi and Kumohira. There, Miharu learns of the hidden ninja world Nabari, the roles of his classmate and teacher in that world, and of the hijutsu Shinrabanshō (森羅万象, Shinrabanshō? lit. "all things in nature") within him. The hijutsu, containing all the world's knowledge, is sorely coveted after in Nabari. And because of that, Miharu cannot return to his normal life. He must become the "Ruler of Nabari" to survive.