明治政府建立二十余年，新时代虽已来临，却似乎与人们心中——尤其是维新志士心中的那个理想国度相差甚远。国家仍处在大时代的动荡惶恐之中，战争的阴影仍笼罩在日本的上空。 当年的浪漫剑客如今纷纷尘埃落定：弥彦成长为正直善良的剑客；左之助也少却了青春孟浪，变得沧桑；剑心的儿子剑路同样拜入比古清十郎的门下，誓要成为绝世高手，却与父亲分外隔膜；剑心接受政府的任务赶赴大陆战场，为了赎回前半生的罪过而疲于奔命，逆刃刀从此封存，家中只留下病弱的阿薰苦苦等待。 这不再是关于明治剑客的浪漫谭，这是一个英雄迟暮的哀婉诗篇……

In 1868, after the Bakumatsu war ends, the ex-assassin Kenshin Himura traverses Japan with an inverted sword, to defend the needy without killing.

Shishio's plan is enacted while Kenshin and Misao help defend the city.

Although she's only sixteen and looks even younger, Misao Makimachi is already a skilled and competent member of the Oniwabanshu ninja clan. That's fortunate for Misao, because her onimitsu talents may be all that keeps her alive when a journey in search of the leader of the clan, Aoshi Shinomori, leads her instead into a face-to-face encounter with an even more dangerous man and a plot to overthrow the Meiji government! Quickly enmeshed in the affairs of the legendary assassin Hitokiri Battosai, now known as Kenshin Himura, wielder of the reverse-blade sword, Misao finds herself pulled into the middle of a deadly intrigue against Makoto Shishio, who is orchestrating the conquest of all Japan - beginning with Kyoto!

The war against the Tokugawa Shogunate ended years ago. But there are some who are not happy with the outcome. Shigure Takimi watched his friends and family get slashed down in the name of freedom and prosperity. Now he and a band of desparate rebels have sworn to settle one final score. Only one man stands in their way: Rurouni Kenshin. Will the former assassin take up his sword to fight again? When Shigure discovers Kenshin's true identity and his fight becomes a personal vendetta, the young hero will have no choice.