Kuro and Benkei, fleeing pursuers, seek refuge in the forest home of Kuromitsu. When Kuro falls ill, Benkei leaves to seek medicine. The pursuers attack Kuro and Kuromitsu, mortally wounding Kuro. Kuromitsu offers Kuro eternal life.

A corrupt wandering samurai attacks Kuro and Kuromitsu in the town near her home and beheads Kuro. Kuromitsu kills the samurai and attaches Kuro's head to the samurai's body. In flashback, Kuro drinks Kuromitsu's blood, but before his transformation can complete, they are attacked by an enemy who has been hunting Kuromitsu for the secret to her immortality. Kuro is beheaded by Benkei, whom the enemy had recruited to be their new leader.

Without any memory of how he got there, Kuro awakens in the forest in a post-apocalyptic world. Upon entering a crumbled city of Asuka in search of Kuromitsu, he meets Haniwa resistance member Karuta. The Red Imperial Army attacks the club fronting for the Haniwa HQ. Kuro attacks the Red Imperial Army when he recognizes their emblem as the same as those who hunted Kuromitsu.

Kuro recovers from the fight with the Red Imperial Army at Rai's apartment. Rai takes Kuro to Izana, who claims he can reunite Kuro with Kuromitsu if Kuro joins the Haniwa rebels against the Red Imperial Army.

The Haniwa take Kuro to meet the rebel leader, Saniwa. She promises to reunite him with Kuromitsu. The Red Imperial Army seeks Kuromitsu's blood to breed an army of enhanced soldiers.

Arashiyama and the Red Imperial Army attack Haniwa HQ and Saniwa's residence in search of Kuromitsu's blood.

Kuro and the Haniwa travel to the underground village of Kagura, but discover the residents slaughtered and Kuromitsu gone.

The Red Imperial sorceress Kagetsu tortures Saniwa to learn the whereabouts of Kuromitsu. Kuromitsu appears, kills Kagetsu, tells Kuro to go to the Red Imperial HQ, and disappears again. Saniwa dies.

Kuro and the Haniwa travel to the Red Imperial HQ in Tokyo. Karuta dies.

Kuro and Rai are captured by the Red Imperial Army. Kuon is revealed to be, among other things, a Red Imperial agent who infiltrated the Haniwa at Kuromitsu's command.

Hasegawa plans to remove Kuro's head for his experiments. Kuro kills Hasegawa. Kuon kills Rai, then tells Kuro that Kuromitsu planned to use his body as Kuro's perfect new body. Kuro kills Kuon.

Kuro confronts the Red Emperor, who is revealed to be Benkei, and kills him. Kuromitsu beheads Kuro and places his head on a new body. Kuro awakens in the forest, having lost his memory, and begins again his search for Kuromitsu.