Miharu Rokujo is a modern-day Japanese student apathetic to the world around him. Miharu for the secret art, Miharu cannot return to his normal life. Although he wants nothing to do with ninja, Tobari vows to Miharu one day, Miharu is protected from ninja by Koichi Aizawa and Tobari Kumohira, who are ninja affiliated with the Banten Village. He learns that his body carries the Shinra Banshou, the most powerful secret art in the ninja world of Nabari. Because the Grey Wolves, a faction associated with Iga village want to use the Shinra Banshou for their personal gain, they will protect him until he becomes Nabari's ruler. Miharu instead asks that the Shinra Banshou be removed, which has never been successfully done. Soon after, Raimei Shimizu, a samurai from the neighboring Fuuma ninja village, arrives to test Miharu's abilities. Eventually, Raimei invites the Banten ninja to see Kotarou Fuuma, the leader of Fuuma village. Because he has written every text on ninjutsu, he may find a way to remove the Shinra Banshou. At Fuuma village, they discover that the Grey Wolves are searching for Fuuma village's forbidden art. The Grey Wolves recognize Miharu as the one who possess the Shinra Banshou, and Yoite, a user of Iga's forbidden art of Kira, attacks. The Grey Wolves escape soon after. With this, the Fuuma and Banten ninja realize that the Grey Wolves are collecting the forbidden arts in the hope of finding a way to remove the Shinra Banshou from Miharu. The Fuuma and Banten follow suit.
After Miharu returns to the Banten village, he is approached by Yoite. Yoite wishes that his existence be erased. If Miharu does not comply, Tobari, Aizawa, and Raimei will die. As Miharu tries to gain enough control over the Shinra Banshou to grant Yoite's wish, Kairōshū, Fuuma, and Banten collect the forbidden arts from the other ninja villages. Meanwhile, Miharu and Yoite grow closer, until it finally becomes apparent to Miharu that he now cares about Yoite, and does not want to erase him. Nonetheless, he continues trying to find a way to control the Shinra Banshou, going as far as to join the Kairōshū, where he becomes close to Raikō Shimizu, Gau Meguro, and Kazuhiko Yukimi. A new character, Shijima Kurookano, is also introduced, with an unexplained physical similarity to the Shinra Banshou. It is later revealed that both she and Kouichi are immortal (and Shijima is also a cat). Eventually the Kairōshū manages to get its hands on three of the four forbidden arts. It is at that point that the manga and anime differentiate.
In the anime, after learning that the Kairōshū will kill Yoite, he and Miharu run away and find Oda, hoping that she will help Miharu control the Shinra Banshou without the Engetsurin scroll. Raikō Shimizu and Gau Meguro both abandon the faction to save Yoite and Miharu. However Raikō is killed in the process. Yukimi, meanwhile, struggles with his loyalty to the Kairōshū and his deep friendship with Yoite. During a Kairōshū attack on Banten, Miharu is controlled by the Shinra Banshou but his mother appears and stops him. Many members of the Kairōshū, including Hattori and Ichiki, are killed in the attack. After five days of resting at the hospital, Miharu searches for Yoite and finds him at the church. Feeling responsible for everything that has happened, Yoite no longer desires to be erased and has chosen to die alone. Miharu however claims that everything is his fault and explains that he wanted to help Yoite disappear if that is what Yoite really wants. After hearing how everyone sees him as an invaluable friend, Yoite decides to live out his remaining days, so that he does not waste the sentiments that everyone has shown him. Everyone then continues on, content with their lives. Yoite simply feels grateful that he met Miharu. Back at Kumohira and Hanabusa’s house later on, Miharu and Yoite are waiting for everyone to come by to visit. Miharu then steps away for a bit to get some lemonade and comes back to find Yoite’s body dissolving into the air. Miharu vows to never forget him.
In the manga, Miharu and Yoite continue to live contentedly with Yukimi, until Hattori decides to take Miharu to live with him. Yoite is noticeably discontented by this action, but Yukimi, who is preoccupied with questions about Yoite's past, does not notice. He leaves to track down Yoite's hometown. Miharu, meanwhile, is pressured by Hattori to give up his desire to grant Yoite's wish. Yoite, who has come to take Miharu home, panicks at this and attacks Hattori. Miharu and Yoite escape, though they are tracked down by the Kasa and have to keep running. They decide to return to Banten. While on their desperate adventure to get there, both finally confront their secret feelings; Yoite admits that Tobari's, Raimei's, and Kouichi's lives were never really in danger. Miharu, in turn, finds that he still wants to help Yoite as strongly as he did before... and must admit that he had been helping Yoite for a long time because he cared about him, not because he was concerned about his other friends. He finally admits to himself and Yoite that he could have used the Shinra Banshou to erase Yoite a long time ago, had he really wanted to. But he is interrupted before he can finish telling Yoite what he really wants: for Yoite to live. Yoite and Miharu manage to get to Banten, where they hide in Hana and Tobari's home. She is up front with Yoite, when he explains that he feels like he isn't alive, telling him that only he can decide what he is - whether he is alive or dead, and who he is. Then she really drives the point home by explaining that everyone helps him because they care for him.
Meanwhile, Yukimi meets Yoite's half-brother, Tsukasa, and learns that Yoite was once named "Sora," a young child who was abused horribly by his father and stepmother, all because his mother died in childbirth. Sora was stabbed in the throat, and would have died then and there had Hattori not discovered and saved him. Kazuho later reveals to him that Yoite is "neither male or female." She then lets him know that Miharu and Yoite betrayed the Kairōshū. Yukimi panicks, and immediately leaves to protect them. He is confronted by Raikō, who calls him a traitor and says he too will be killed if he goes to help them, but Yukimi goes anyway. Back at Hana's house, Miharu is kidnapped by the Kasa and Yoite must go to save him. He is accompanied by Shijima, Kouichi and Raimei. Kouichi is revealed to be an owl at this point, as well. There is a long battle, and eventually Raikō and Gau also leave the Kairōshū in order to save Miharu. After fighting for a while, Yoite eventually finds and saves Miharu. After being protected by Yukimi (who loses an arm in the shuffle), the two manage to escape. Remembering Hana's words to him, Yoite has a revelation. He becomes content with himself, and loses the desire to be erased. As he decides to himself, "I am Yoite!" He becomes satisfied with the Yoite that Miharu and Yukimi both loved so much. He, however, is slowly dying. Miharu is horrified, and wants to use the Shinra Banshou to save Yoite, but the latter states that he has killed too many to be saved. He smiles, content in his friend's arms, and implores Miharu to erase him if Miharu thinks he will be unable to go on without him. He then dies in Miharu's arms.
In the next chapter, Miharu wakes up to discover he has been in a deep sleep for weeks. It is revealed he has become the King of Nabari by erasing somebody. However the erasure was not complete because people can still feel traces of "that person" - namely Yukimi and Miharu, who are both suffering from an unexplained loneliness. Miharu even has a breakdown because he misses Yoite so much. However, months pass, and he grows closer to Yukimi in particular. The members of Banten - as well as Kazuho, Yukimi, Fuuma, and Shijima - band together to find a way to use the Engesturin to remove the Shinra Banshou from Miharu's body. Meanwhile Raikō, Gau and Raimei, also on Banten's side, return to where the Shimizu home once stood, vowing to start the Shimizu family again. Eventually Kazuho and Tobari devise a method that they think will work, and go to use it. Tobari first reveals what happened ten years ago; he and his grandfather attempted to remove the Shinra Banshou from Miharu's mother, Asahi's body... But before they could, Miharu's father Akatsuki was killed. Tobari's grandfather was then also killed. Miharu himself, then only four, was attacked and killed by a mysterious cloaked figure. Asahi went insane from this shock and brought Miharu back to life - but at the apparent loss of her own life, and the Shinra Banshou then transferred to Miharu. Tobari also reveals that Raimei and Miharu are second cousins (Kourin and Asahi were first cousins). Before he can actually attempt to draw the Shinra Banshou from Miharu, the cloaked figure appears. This same figure, called Inasa, is a Kira-user who has been given temporary conrol of the Kairōshū by Hattori. Tobari immediately recognizes this is the same person who killed Miharu all those years ago. His hood falls back, and it is revealed that it is Fuuma. Everybody is shocked and horrified.
Miharu is also shocked, and withdraws into himself, where Asahi battles with the Shinra Banshou. The Shinra Banshou wants Miharu to remain apathetic, while Asahi wants her son to trust people again. Eventually Miharu realizes he doesn't have to hide from people anymore, and grows more confident. Asahi is pleased with her son, and vanishes. The Shinra Banshou decides to return everybody's memories of ten years ago, noting that there are still "lies" in Miharu's heart. Meanwhile, Ichiki has also remembered what happened ten years ago - and, for some reason, this prompts her to kill Hattori. She then opens her eyes for the first time, suggesting that she is not blind after all. She decides to return to where the Shinra Banshou is, clearly planning something. Fuuma meanwhile explains that his goals are to attain wisdom beyond human knowledge, and essentially "become God." Tobari is extremely hurt by his betrayal, and attacks him. Raimei and Raikō also return to protect Miharu, making it clear they will no longer be on Fuuma's side. Shijima and Kouichi, too, call off their long alliance with Fuuma. The chapter ends with Tobari being horribly wounded by Fuuma; it is unclear as of yet whether he will survive.