Ten years after the start of the Meiji Era, a Rurouni wanders into Tokyo to find a new life with new friends. Vowing never to kill, he tries to escape his past as the Hitokiri Battousai, the greatest killer of the Bakumatsu.

However, an old menace, in the form of Shishio Makoto, the successor to the Hitokiri Battousai, threatens the peace of the new Meiji Era. Shishio and his Juppon Gatana are ready to start a new revolution to correct the evils of Western influence.