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

An old menace threatens the new Meiji Era, the villian is Shishio Makoto, the successor to the Hitokiri Battousai who was supposed to have died in the Boshin Wars. Shishio and his Juppon Gatana are ready to start a new revolution to correct the wrong doings of the Meiji Government and also to avoid colonization.