Kenshin then goes back home, and a few days later, the leader of the Ishin visits him, telling him that it is time to take up his sword once more. Kenshin does so, and when the Ishin Shishi finally win, he trades in his daisho for a sakabatou and wanders as a rurouni. He wanders through ten years of the new Meiji restoration, until he meets a girl named Kamiya Kaoru ^_^ who lets him stay at her dojo. Over time, they are joined by Myojin Yahiko, an orphaned boy with the blood of a Samurai, Sagara Sanosuke, the streetfighter, and Takani Megumi, the doctor…

This is basically the point where the manga's first issue begins, and after a few minor storylines, the Shishio story arc begins.

This arc, in a nutshell, is where Kenshin's successor, Shishio Makoto, comes back to take over Japan. (After Kenshin retired the Hitokiri inside of him, the Ishin Shishi had to find a replacement for their best assassin. The man they chose was the cunning, razor-quick Shishio Makoto. However, they were unable to control him, and as such ordered his death. He survived, however, and ended up being horribly burned all over his body.)

This arc begins with the introduction of Saitou Hajime, another old ghost from Kenshin's past. He was the fourth captain of the ShinsenGumi during the Bakumatsu, and one of the Battousai's main adversaries.

In any case, Saitou is now working as a Police Officer for the government, and he is heading the investigation surrounding Shishio (read: it's his job to kill Makoto). Under orders, he goes to Kenshin to enlist his help, and after a brief fuss, Kenshin eventually agrees. They separate on the way to Kyoto, however, and on one of the lesser-populated areas of Kenshin's path, he meets Makimachi Misao.

Misao actually tries to rob him, but Kenshin being Kenshin, befriends her instead. They eventually end up travelling to Kyoto together, since Misao lives there and decides not to let him out of her sight.