A tale of wandering and vengeance by Hai Itto, a master of the Suio style of swordsmanship and a former official intermediary, wage a one-man war along with his infant son, Daigoro against Yagyu clan.

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.

The heavy rains are causing the rivers to overflow and keeping Daigoro and Itto from moving. While watching children play at the rain shelter, Itto remembers a happy past of his child many years ago.

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.

The lone wolf received an assassination request to avenge a clan on the brink of being abolished. The plot thickens as they got caught in a scheme full of betrayals and deceit while being pursued relentlessly by the Yagyu clan.

The lone wolf and cub found themselves trapped in an inn as hostages, as a ruthless gang of bandits called The Flying Beasts terrorize the village. The lone wolf must now try to break free and save himself, Daigoro, and the other hostages from these bandits.

Ogami and Daigoro are joined in their travel by a runaway prostitute who is being chased by a group of bandits who have been holding her captive for many years. The prostitute developed a strong bond with daigoro who has always longed for a mother's love that he has never experienced.

The Yagyus continue to use any method necessary to kill the lone wolf. Meanwhile, Ogami is shocked to receive an assassination request from a woman with uncanny resemblance to his late wife.

The lone wolf receives an assassination request to eliminate a feudal lord from a member of his own clan. The Yagyus are using this opportunity to hunt down the lone wolf and exploit the clan's weakness at the same time.

The lone wolf is gravely injured during an attack by an assassin group sent by The Yagyus and got separated from Daigoro. In the meantime, Daigoro is being held captive by a corrupt official for assaulting his son.

The lone wolf made a promise to a dying undercover Yagyu ninja, to bring his wife to be together with him in the afterlife. This promise led Itto to a village with only women, whose sole purpose is to give birth to new ninjas.

Itto has become the most wanted criminal in Japan. An old ally who is still in love with Itto helps them pass through the village border by disguising them as members of their own troop.

Itto received an assassination request to kill a feudal lord and was betrayed by a traitor in the clan. Daigoro was ambushed and the two of them got separated. In their times apart from each other they learn more about family bonds and what it means to become a parent.

During the time when christianity was punishable by death in Japan, Lord Retsudou threatens to persecute a clan leader's wife, who is secretly a Christian. The clan leader, who is a former disciple of the lone wolf, has no choice but to fight his old master.

The lone wolf receives a request to kill a traitor who is responsible for the abolishment of a clan. The mission led him to unveil a cruel betrayal in a tragic story between a dying wife and an undercover ninja.

While passing the shrine, Itto and Daigoro saw a strange man (Sakon) smiling with only his head sticking out from a stand. He was holding up a banner that read, "This head is for sale.”

Itto is asked to avenge a daughter's murder by an oshichiri impostor. While seeking shelter from the rain, he encounters a woman named Otoshi and witnesses an oshichiri attempting to attack her.

The Otawara clan faces financial strain due to poor harvests after their leader, Kiyotada, passes away. Hirabayashi, in charge of finances, imposes a 20% increase on farmers, leading to unrest. The farmers debate whether to appeal directly in Edo or rebel against the clan's decisions.

Ugenta, a Yagyu subordinate, attacks Itto. Daigoro clings to Itto's back while fighting Ugenta. Itto loses his position and Daigoro falls down a cliff.

Itto and Daigoro set up camp deep in the mountains to investigate the Yasha-masked woman.

Itto and Daigoro were walking, when Yagyu's Unsui and his men attacked Itto fiercely. Itto managed to hold off Unsui, but he was caught by surprise, and an iron claw at the end of a staggered iron chain struck Itto in the shoulder, causing a deep wound.

As Itto and Daigoro were making their way along a country road, they came upon a procession of palanquins. Suddenly, young warriors and peasants with swords and side arms attacked the palanquin procession. However, Minowa, the warrior guarding them, was strong with his sword. In no time at all, he had cut them down.

Ittou was to continue his journey with Yayoi. Komakine went to Retsudo. To his surprise, the request for an assassin for Itto was sent by Retsudo. When Komakine reported his conversation with Itto to Retsudo, he was poisoned and killed. What was Retsudo up to?

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 an assassination request to kill a clan leader from a grieving widow of a samurai. Knowing the danger that lies ahead, he left Daigoro in case he does not survive the mission.

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.