A mysterious wanderer known as Kenshin is taken at the Kamiya Kasshin Dojo, a martial arts school run by a young woman named Kaoru.

Following an encounter with a young pickpocket named Yahiko, Kaoru risks her own freedom to gain his from some local gangsters.

After reining in some renegade police officers, Kenshin is recognized as the Samurai whose bravery helped establish the Meiji Era and is asked to rejoin the army.

Gohei enlists a vicious street-fighter known as Sanosuke to seek revenge against Kenshin. And even though Kenshin exposes Gohei's plan, Sanosuke makes it clear that the two of them will fight each other one day.

After accepting Sanosuke's challenge, Kenshin encourages him to release his anger towards the corrupt Royalist forces.

With a ruthless ex-Samurai killing high ranking politicians, the Chief of Police asks Kenshin to catch him. But as Kenshin confronts the deadly Jin-nai Udo, Kaoru's efforts to stop the battle end with her kidnapping.

After kidnapping Kaoru, the ruthless Jin-nai Udo draws Kenshin into the fight he's been seeking for years. Though Kenshin tries to resist, Jin-nai's powerful spell over Kaoru leaves him no other choice.

When local gangsters threaten the life of a beautiful woman, Kenshin and Sanosuke step in to save her.

Though her medical knowledge has saved Yahiko's life, Sansosuke suspects Megumi of producing the opium responsible for a close friend's death.

Having pledged to save Megumi, the Peace Force must first take on a band of ruthless drug dealing mobsters. But when a rift inside the gang leads to a change in leadership, Kenshin must confront a fighter whose powers he's underestimated.

A persistent nightmare comes true when Kenshin's old enemy, the former leader of a shadowy anti-Royalist organization, is hired to assassinate him.

Saito sets a trap for Kenshin by enlisting another assassin in his plan. And once Kenshin repels the accomplice, he's left to take on his old rival.

After stopping a fatal battle with Hajime Saito, a top government official asks Kenshin's help in killing a shadowy assassin who's threatening the future of the regime.

While preparing to give his decision on helping to kill Shishio, Kenshin learns of the Home Minister's murder.

Following Kenshin's departure from the dojo, everyone, and especially Kaoru, are sad at being left behind. And while Saito tries to dissuade Sanosuke from following him, Megumi sends Kaoru to deliver some medicine that will aid in Kenshin's fight .

In the wake of Kenshin's departure, everyone at the dojo is anxious to join the battle against Shishio. With Sanosuke, Kaoru and Yahiko in pursuit, Kenshin encounters Misao, a young girl who also happens to be a clever thief.

After befriending Misao, Kenshin insists that she return the money she's stolen before letting her accompany him on his quest to stop Shishio.

When he and Misao come across a village terrorized by forces loyal to Shishio, Kenshin enlists Saito to help liberate it from the evil gang.

Leaving Misao behind, Kenshin and Saito make their way inside Shishio's fortress. Following a confrontation with one of his most powerful henchmen, Kenshin is ready to take on Shishio himself.

Following Kenshin's defeat of the giant Senkaku, Shishio pits him against the young, emotionless assassin responsible for the Home Minister's murder.

Back at home, Kaoru works to restore the dilapidated dojo, while Kenshin encounters a wise old fisherman who teaches him an important lesson about love.

After stepping in to stop what appears to be a robbery, Kenshin and Kaoru meet a young prince who looks exactly like Yahiko.

Sanosuke adopts a stray dog, unaware that it holds the key to a criminal gang's plot to blackmail some local officials and gain political control. And when the gang finally tracks him down, Kenshin and Yahiko join Sanosuke to foil their plan.

After Kenshin finds a ring inside a catfish, he's persuaded to give it to Kaoru. Thinking it's an engagement ring, Kaoru is sure that he's asking her to get married.

Alerted by Misao, Kenshin and the rest of the Peace Force arrive to help Aoshi find a mysterious killer. Kenshin's investigation uncovers evidence linking the killing to a Christian Samurai and of vengeance that's been foretold.

In an effort to prevent more revenge killings, Kenshin must take on Shogo Amakusa, the Christian warrior known as God's Child.

As Kenshin prepares to honor his promise to stop Shogo Amakusa, he and Sanosuke uncover a secret church that was built when Christian worshipers were forced underground.

When neither Kaoru nor Kenshin can persuade Shogo Amakusa to abandon his plan to advance the Christian cause through violence, the stage for battle is set.

Though blinded by his duel with Shogo Amakusa, Kenshin seeks another battle in hopes it will restore his sight.

Along with the story of his parent's martyrdom, Misao uncovers the truth behind the alleged miracles that deified Shogo Amarusa.