Itto and Daigoro have officially become the most wanted criminals in Japan. Retsudo is enraged and send his own estranged son to lead an elite assassination squad to kill Itto before other people can claim the bounty.

A disgraced samurai intercepted an assassination request made to the lone wolf. Itto now has no choice but to go against a deceitful woman and her cunning plot to make her daughter the heir to a clan.

Itto receives a request to track down and kill a group of ruthless bandits from Edo. He crosses paths with a skilled private investigator who swore to get to them first before anyone.

The lone wolf and cub continued to attract bounty hunters wherever they go. Their journey brought them to a town heavily guarded by the elite guards of the shogunate, where they met a traveling couple on a revenge mission.

The lone wolf receives a request to assassinate a ronin who is believed to be plotting a rebellion to overthrow the reigning commander. Meanwhile, Daigoro forms a bond with the very ronin his father is supposed to kill.

The lone wolf and cub, officially the most wanted criminals in Japan, continue to attract the attention of bounty hunters. The retainer of a clan just increased their bounty to 2000 ryo, gaining the interest of some of the most ruthless bounty hunters in the area.

Itto receives an assassination request to kill a disgraced samurai which he had fought in the past. While the Yagyus keep pulling the strings from the shadows, Itto might have finally met his match.

Itto's journey finally leads him back to Edo to confront his arch enemy. The two rivals are racing to get their hands on an encrypted scroll, containing all the secrets that the Yagyu undercover ninjas have gathered from all 64 provinces that Retsudo would use to blackmail the whole country into submission.

Upon securing the Yagyu encrypted scroll, Itto quits his life as an assassin and dedicates himself to decipher the scroll and expose all of Retsudou's evil plan. The long battle is finally reaching its climax as the lone wolf faces the Yagyu clan in an inevitable duel.