Learning that Shishio is in the village at this time, Kenshin and Saitō pay Shishio a visit and are followed by Misao and a young orphan boy whom Kenshin rescued, named Mishima Eiji, who's family are the victims of a powerful henchman of Shishio, named Senkaku. They later head to Shingetsu village, controlled by Shishio, where Kenshin meets Saitō once again. Kenshin hides the truth from Misao, knowing that news of the deaths of Aoshi's students (her former comrades, whom she looked up to as a child), would wound her deeply. He later learns that she is a member of the Oniwabanshū Ninja clan, who is searching for Shinomori Aoshi, the clan's leader and Kenshin's former adversary, whom he defeated in a hard-fought battle in Tokyo a while ago and his 4 students ( Beshimi, Hyottoko, Shikijō and Han'nya). On the way to Kyōto, Kenshin meets a young tomboyish girl named Makimachi Misao and is surprised by her combative skills. During the training he is visited by the spirit of his former mentor, the deceased Sagara Sōzō, and by the end of one week, he masters the technique of Futae no Kiwami, with his right hand, which deeply impresses Anji. Upon seeing Anji using turning figures of solid stone into dust, by slamming his short sword into the ground, Sano asks that he train him, to which Anji eventually agrees. On his way to Kyōto, Sano keeps getting himself lost in the middle of nowhere, until he meets Yukyuzan Anji, a fallen Buddhist monk. Sano still refuses to give up, saying that Saitō's attacks don't hurt nearly as much as him being treated by Kenshin as his weakness and so Saitō let's him that he can do whatever he wants and heads off. This infuriates Sano, who tries to attack Saitō, but is once again beaten up by him, even when Saitō plays Sano's game and fights in hand-to-hand combat, putting his sword aside.
Sagara Sanosuke, likewise heads towards Kyōto, although Saitō confronts him just as he is about to leave telling him that he is a weakness for Kenshin and that if he goes to Kyōto he'll only get in the way, because he is not strong enough to be battling Shishio and his henchmen. After moping and not eating for a few days, Kaoru is harshly reprimanded by Takani Megumi and Myōjin Yahiko influences her to travel to Kyōto along with him in the hopes of finding Kenshin and bringing him back to Tokyo. He is thus forced to say goodbye to Kamiya Kaoru and renew his journey as a Rurouni. Okubo is later killed by Shishio's top henchman, Seta Sōjirō, just as Kenshin goes to meet him and this prompts Kenshin to go to Kyōto and thwart the plans of Shishio. After no clear decision is made, Okubo asks to meet Kenshin on the 14th May, so that he can make his final decision. Kenshin is asked by Okubo to head towards Kyōto and kill Shishio Makoto, the man who took over his duties as Hitokiri, in the shadows and is now planning to create a new Japan, where only the strongest survive, with himself as its absolute overlord. Okubo Toshimichi, the leading politician in Japan, appears along with Kawaji in the Kamiya Dōjō where the battle is being held and at the final moment Kawaji's voice prevents Saitō and Kenshin from killing one-another (since they are so deeply absorbed in the battle, that they are unaware of their surroundings and can only hear the voices of those, who like themselves, have witnessed the horrors of the Bakumatsu). The arc begins when Kenshin is confronted by his old adversary, Saitō Hajime, who is now a Lieutenant of the police force and appears before Kenshin as an enemy once again (though in reality, he is simply commanded to test Kenshin's abilities by police commissioner, Kawaji Toshiyoshi).