After finishing his job as the murderer "Hitokiri Battōsai" in the Ishin Shishi, Kenshin assumes the life of a wanderer. Ten years after the Revolution, he arrives in Tokyo, where he meets Kaoru. She invites him to stay in her dojo even after she discovers that Kenshin is the "Battōsai". During his residence in the dojo, Kenshin establishes lifelong relationships with many people, including ex-enemies. When Shishio Makoto, the brutal once-successor to Kenshin's position as Chōshū's hitokiri, masterminds a movement seeking to overthrow the Meiji Government, Kenshin leaves Tokyo to stop him. To defeat such a foe, Kenshin is forced to resume his training and mend his relationship with his teacher Seijūrō, who taught and took care of Kenshin, originally named Shinta (心太), in his childhood. That childhood training was interrupted when Kenshin decided to protect the people of Japan. After finishing his training, all Kenshin's friends reunite with him and help him to defeat Shishio and his army.

Months later, a man known as Yukishiro Enishi starts attacking all people that Kenshin meets as an act of revenge for the death of his sister Tomoe. At this moment, it is discovered that Kenshin was married to Tomoe in the Bakumatsu but accidentally killed her when trying to rescue her from a group of assassins. When Enishi finds out about Kenshin's feelings towards Kaoru, Enishi sets out to kidnap her. He succeeds and leaves behind a professionally-made decoy of Kaoru with a sword in her heart, making everyone believe that she had been murdered. Kenshin falls into severe depression and runs off to a village of wanderers to mourn. However, he breaks out of his depression after his friends discover Kaoru is alive. The group goes to rescue her on Enishi's island. A battle between Kenshin and Enishi follows and when Kenshin wins, he and Kaoru return home. Five years later, Kenshin is married to Kaoru and has a son named Kenji. After an encounter with Kaoru's student Myōjin Yahiko, Kenshin gives his sakabatō to him as a gift for his coming-of-age.