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Fourteen years after defeating the immortal warrior Himuro Genma and thwarting the Shogun of the Dark's evil plans, Kibagami Jubei continues to roam all over Japan as a masterless swordsman. During his journey, he meets Shigure, a priestess who has never seen the world outside her village. But when a group of demons destroys the village and kills everyone, Jubei becomes a prime target after acquiring the Dragon Jewel—a stone with an unknown origin. Meanwhile, Shigure—along with the monk Dakuan and a young thief named Tsubute—travels to the village of Yagyu. And with two demon clans now hunting down Shigure, Dakuan must once again acquire the services of Jubei to protect the Priestess of Light.

Jubei Kibagami wanders feudal Japan as an itinerant swordsman-for-hire. After a past betrayal left him masterless, he has no more patience for warring political factions and their schemes. Unfortunately, both past and political intrigue collide when he meets and saves a female ninja named Kagero from a man with the ability to make his body as hard as stone. The sole survivor of a ninja clan, Kagero continues her team's last mission: investigate a mysterious plague that wiped out an entire village. Jubei wants nothing to do with this, but the stone-like man's allies, a group of ninja with supernatural powers known as the Devils of Kimon, make that option difficult. To make matters worse, a government spy poisons Jubei, promising him an antidote if he can unravel the true intentions of the Devils of Kimon and their connection to the plague. The trail leads to shadow leaders, a plot to overthrow the government, and a man that Jubei thought he would never see again.