11th year of the Meiji Era in downtown Tokyo. Kaoru Kamiya, the acting master of the “Kamiya Kasshin-ryu” style, was chasing after the “Hitokiri Battosai,” who was claiming to be a user of her sword style. One night, Kaoru meets a man carrying a sword. She immediately questions the man, but he seems to have absolutely no will to fight. “Is this the rumored Hitokiri Battosai?” As Kaoru dubiously looks on, the man introduces himself as Kenshin Himura, a “Rurouni.”

Kenshin sees a dream recalling the Shinsengumi, who he faced off against back when he was a Revolutionary warrior. The Shinsengumi was a group of highly skilled swordsmen who he fought on equal footing back when he was the Hitokiri Battosai. He feels unsettled and ponders why he is suddenly remembering them. As the tension persists, a mysterious man with very unique-looking eyes pays a visit to the Kamiya Dojo while Kenshin, Kaoru, and Yahiko are not home. When he meets Sanosuke, who just happened to be at the Dojo, he claims that he is Goro Fujita, a medicine seller, but...

After defeating Arundo Akamatsu, Kenshin returns to the Kamiya Dojo and sees Hajime Saito. Hajime had introduced himself to Kaoru and Yahiko as Goro Fujita, the police officer, and they had invited him into the Dojo without any suspicion. Hajime criticizes Kenshin and the others for their naivety. Over the past ten years that Kenshin had washed his hands of manslaying, Hajime had honed his killing intent and skills as a hitman, and now Hajime's ferocity was aimed at them.

The person who had sent Hajime to face Kenshin was none other than the Head of the Home Ministry, former Satsuma Domain Revolutionary warrior, Toshimichi Okubo. He asks Kenshin to go to Kyoto to stop the secret plans of a man who claims to be the legitimate successor of the Hitokiri Battosai. However, that man was supposed to have been killed 10 years ago by his own comrades in the government, as they regarded him as a threat. Receiving this request to conduct an assassination, what will Kenshin's answer be...?