Plot:
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.

Characters:
Miharu Rokujo
The protagonist of series, Rokujo is a 14-year-old middle school student. He holds Nabari's hijutsu, the Shinrabanshō, in his body. He pretends to act indifferent to those around him in order to protect them from getting hurt, though he is not averse to acting in a rather innocent and cute way in order to get what he wants. He remembers little of his childhood, and had lost his parents at a young age. His only goal is to inherit his family's okonomiyaki store.

Thobari Kumohira Durandal
Rokujo's and Kouichi's 25-year-old teacher in the "front world". Born in Ireland, Kumohira is actually a ninja of the Banten village in the world of Nabari. He is entirely devoted to protecting Rokujo, and wants him to become the ruler of Nabari. He has an intense hatred of transport, such as trains and buses, and would not get on one until Rokujo manages to "persuade" him. He went to Japan because his grandfather was a "Japan otaku" and "ninja fanatic", who forced him to go to learn to become a ninja, and was unable to return home for ten years (partly due to his phobia of vehicles). In the anime, he is the temporary leader as the current leader is away, while in the manga, he is not just a stand-in, but actually has the power to arrange for a temporary leader. According to Aizawa, Kumohira has probably recorded Banten's kinjutsu through verbal communication.

Kouichi Aizawa
Rokujo's 14-year-old classmate who studies nindō under Kumohira. Though he normally has an energetic attitude when around others, he is serious and relentless when it comes to his ninja duties, and is apparently fascinated with death. It is later revealed that his love of death is a result of his own inability to die. His immortality is attributed to the holder of the Shinrabanshō during the Edo Period, who was a medical practitioner, experimenting with placing the wisdom of the Shinrabanshō into animals, since humans usually died. There were only two survivors of the experiments, both of whom gained immortality as a result. Kōichi's ultimate goal is to find a way to die, as well as ensure that "monsters like [himself] are never created again."

Raimei Shimizu
She is a 14-year-old guardian of the world of Nabari, and the head of the Shimizu clan. She is also a Fūma-nin (風魔の忍, Fūma no nin?, "Wind Magic/Demon Ninja") who prefers fighting with a sword (named Kurogamon (黒我聞, Kurogamon?)) over using ninjutsu, claiming to be a samurai. She has the tendency to mistake one person for another, or reveal information she means to keep to herself, when excited. Five years ago, her older brother, Raikō, annihilated their clan, and she has sworn to kill him in revenge.