Miharu Rokujou is asked by his classmate, Kouichi, to join the school nindou club. After refusing, Miharu is asked by his English teacher, Kumohira, to join the club. Although the two look like a student and teacher, there's more to Kouichi…

Now a part of the nindou club, Miharu continues his indifferent ways and doesn't really participate in training. Much to Kouichi's and Kumohira's disappointment. When a girl samurai named Raimei Shimizu comes to see if Miharu would be a goo…

Miharu and the others arrive when the Fuuma village is under attack. Although the group takes out a couple of the enemy ninja, they are easily defeated by the strongest of the group. Will Miharu have to use his hijutsu to save himself and e…

After chasing Yoite off, Kotarou has the remaining Fuuma ninja treat the wounded while he makes up causes of death for the dead. Thanks to the Fuuma ninja, Miharu's group is treated of their injuries and even Kumohira is saved. Later, after…

Finally back in Banten, Miharu, Kouichi and Raimei destroy Banten's ninja skill books. Later, trouble arises when Miharu's teacher and former Kairoushuu member Masami Yamase appears. Kouichi and Raimei come to his rescue, but when Raimei fi…

After regaining consciousness Raimei and Kouichi begin searching for Miharu. After not being able to find him, they seek out Kumohira, who has just arrived in Banten. Although Kumohira wants to search for Miharu immediately, Kouichi points …

Yae Oda, the leader of Togakushi, arrives in Banten, with Katou Sourou. They have a unique offer for Miharu and his group. In exchange for assassinating the CEO of a company that does more then it says, Yae will give them Togakushi's kinjut…

As Miharu searches for Kumohira, he is caught by Yoite and Yukimi. Meanwhile Kumohira attempts to assassinate Frosty, but is stopped when Yoite and Yukimi show up with Miharu. As Frosty and his men try to escape, they are attacked by Yae. W…

A murder brings Raimei closer to finding Raikō. Aizawa is dispatched to stop Raimei from doing anything drastic. Miharu stays with Kumohira while his aunt is away. Meanwhile, the Kairōshū gathers. Yoite begins to show signs of his life forc…

Raimei and Raikō confront each other and Raikō wounds Raimei, but not fatally and takes her sword, Black Gamon, with him. Yoite is found by a woman who stays with Kumohira. She brings him home and treats him kindly, but the feeling is not r…

Raimei, released from the hospital, wants to retrieve the Black Gamon. She and the group encounter Gau, a member of Kairōshū. At Raimei's home, he tells her the truth about the day Raikō killed the Shimizu. Raimei returns to the site of the…

When Miharu goes to visit Gau, Raimei tells him that Thobari told her about his promise to Yoite and says she'll help him. Miharu meets up with Yoite and retrieves the Izura Shingan scroll. He later announces to Kairōshū that he is joining …

Representatives of Kairōshū and Banten reach Alya academy located in the Kouga village to discuss the future of the world of Nabari and are welcomed by the students of the academy since the leader of the village is on his deathbed. Secretly…

Miharu and Yoite run from the academy students as Yoite is injured. One of the academy teachers, who is also trying to get the kinjutsu scroll, shoots Aizwa. It is revealed that Daya, the kinjutsu capable of curing anyone, requires the fles…

Miharu tries to save Yoite, but Thobari doesn't approve of his using the Shinrabanshō and knocks him unconscious. Aizwa, seemingly immortal, rescues everyone. Before dying, the headmaster entrusts the kinjutsu scroll to Shijima who in turn …

Aizawa reveals his immortality to Thobari and Raimei. It is revealed that Hattori does not need Yoite if he outlives his usefulness. Miharu and Yoite visit Hanabusa to discover the location of the Engetsurin. Thobari does not return at nigh…

Yukimi visits Hanabusa to search for Thobari. Upon finding she does not know anything, he eventually leaves. The next day, Raimei visits Kouichi, telling him she is helping Miharu obtain the kinjustsu Engetsurin. The pair are suddenly attac…

Yoite's health is failing and he ends up in a hospital. He overhears the doctor telling Miharu that he has about a month to live. Scared, Yoite leaves the hospital, but not before using Kira on Gau, who was still in a coma. Gau recovers due…

Yukimi recalls how he met Yoite, while Gau and Raikou, along with Miharu visit Yukimi. Gau thanks Yoite, and he ends up staying with Yukimi. After, They both leave, looking For Oba, while it shows the 'Intelligence group."

Tobari recalls how he was entrusted with Miharu ten years ago. Miharu and Yoite meet Yae, and Miharu convinces her to use the Izura Shingan to confront the Shinra Banshou. Shinra Banshou tells Yae and Miharu's inner self that she is not gra…

Off in a room somewhere, Yoite wakes up to find himself bound and drugged, but is unaware of where he is. Back at the Kairoushuu hotel, Ichiki, the leader of the Tattegami, tells Hattori how Yae continues to ask about the annihilation of th…

Behind the scenes, Kotarou plans a rescue for Yae along with his subordinates. Kato personally infiltrates the Kairoushuu hotel and finds Yae however discovered by Raiko. Raiko lets them both escape and he confronts Hattori, hoping to cover…

Having brought Yoite and Miharu to Hattori, Yukimi uses the excuse of making the two repent to cover what he did. While Hattori explains how he convinced Yoite to learn the Kira, Raiko finds Ichiki, but before he can do anything he is attac…

After seeing Raiko's body, Raimei and Gau try to attack Hattori, but are easily defeated. Hattori then blames everything on Miharu, who begins to believe it is actually his fault. Acting on his desires, the Shinra Banshou begins to awaken, …

After killing Hattori, Yoite goes into a state of insanity and destroys Hattori's body with his Kira. Meanwhile the Shinra Banshou convinces Miharu to use her powers which results in him growing many times his normal size. Right as things a…

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 Y…