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.

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 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.

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.