Ronin Ogami Itto travels around 17th century Japan, accompanied by his young son Daigoro, in search of those who has offended him.

Daigoro wakes and Itto is gone at the request of Kizaemon to avenge the death of Yoichiro. As a 3-year-old alone, Daigoro is lured to a temple where he meets a pickpocket, Oha and trouble ensues.

While eating at an inn, Itto and Daigoro are visited by Okayo, with blood on her hands from her attacker Bunbematsu, who she accidentally killed. She is protected by Itto, who refuses to turn her over to Torizo, the brothel manager.

Hatsuuchi Suzuki, an official of the Tateyama Clan's Edo residence, attacked the axe-suke of Oshu, an Orizuke, and was beaten to death in a vicious revenge attack. Ittou, however, arrived a day too late. Itto met Hatsuuchi's children, Aya and Soichiro, who appealed to him for revenge. Itto slays Rikuzo in the gambling hall and kills Asuke.

While receiving a request to assassinate in the Ararenji Temple from Saeki, Itto is shot with a poison arrow by the Ura Yagyuans in the form of Unsui, led by Ishine and sent by Yagyu. Meanwhile, while caring for Itto in a coma, Daigoro meets Saya and Lori, a couple that lost a child and becomes fond of Daigoro while Itto’s fate is uncertain.

When Itto received a request from Mitsui, the feudal lord of the Ueda domain, to assassinate him, Daisuke Kasama, a samurai who served him as an attendant, thought it his duty to protect the lord of the castle, and attacked Itto. As he staggered back, Kotani, who had also been accompanying Itto, slashed him with his wakizashi. As Itto cut Mitsui down and turned to leave, Daisuke pleaded with Itto to stop, out of a samurai’s compassion, Itto put a stop to Daisuke.

Tachibana was a prison official, that was at odds with Nui's father. Itto accepted the assassin's request and broke into the prison. What awaited Itto in prison was torture in the name of "sakudukuri" by the prison master, Tensatsu.

Yagyu retsudo had placed people called "Kusa" in various places. "Kusa" were spies who infiltrated the territory, took root as local people, and continued to lead a steady, normal life while investigating the inner workings of the clan in great detail. This job was hereditary and sadly passed down from father to son.