Manji visits a priest in order to confess his sins, namely killing his lord and 100 of his retainers, an act that earned him the moniker "Killer of 100." The priest, who is actually a con artist, attempts to kill Manji by shooting him in the forehead, but Manji kills him and regenerates the wound. Manji returns to his home to find Yaobikuni, a nun who placed "sacred bloodworms" into Manji that make him immortal, and his sister Machi. That evening, Machi dreams of the time when Manji was forced to kill her husband, a police officer purusing Manji, causing her to lose her mind. After the dream, she wanders into the night and is captured by a group of ronin led by the brother of the priest Manji had killed. Manji pursues Machi but is unable to prevent her from being killed. In response, he kills every member of the ronin group, and upon returning to Yaobikuni, declares that he will seek redemption for the 100 men he killed by killing 1000 evil men.

More details about the tragic demise of Rin's family and their dojo are shown during her encounter with Manji. Members of the Ittō-ryū and the Mugai-ryū are introduced, too.

Rin tries in vain to hire Sori, an artist. His house is attacked by minions of the Ittō-ryū, which makes him reveal his true colors.

The tragic past of Taito Magatsu, another member of the Ittō-ryū, who is a target of Rin's vengeance, is revealed. He attempts to lead a normal life by leaving the Ittō-ryū, but encounters Rin and Manji.

Members of the Mugai-ryū are assassinated by members of the Ittō-ryū. Manji an Rin encounter Eiku Shizuma, who reveals Manji's and weakness.

Manji settles the score with Shizuma and receives information about Anotsu's whereabouts.

Rin and Manji encounter Makie Otono-Tachibana, whose life Manji spares, since she appears to be too weak to pose a threat. Furthermore her relationsship to Anotsu is explored.

More details from Anotsu's and Makie's past are revealed. A fierce battle between Manji and Makie unfolds. Afterwards the latter leaves Anotsu and the Ittō-ryū.

Rin and Manji encounter Araya Kawakami, one of the men who raped Rin's mother. His past is revealed and after Rin bravely saves his son, she goes unarmed to his house.

Rin confronts Kawakami emotionally, but is assaulted by him. Manji comes to her rescue and exacts her vengeance. Rin succeeds in foiling his son's plan to continue living for revenge only.

Manji and Rin travel to the house where he lived with his sister and he continues to train Rin. During a break she encounter Anotsu in a nearby forest. After her futile assassination attempt he discloses to Rin the reasons for the animosity between her father and him.

The paths taken by all the surviving characters are shown. Rin abolishes her hesitations and trains with utter devotion. Meanwhile the tactics of the Mugai-ryū seem to have sealed Anotsu's fate.