Edo Era, the world of the Tokugawa Shogunate. There were those who crept in the darkness. The Hiruko Ninja. They are fated to live in darkness, and die in darkness. However, if the power of the Dragon's Jewel, which has been handed down among the Hiruko since ancient times, is combined with that of the Priestess of Light, even the Hiruko can be bathed in light. There was one who, believing this, ran away from the Hiruko. And thus begins our story.
At the same time, a group of ninja called the Kimon Shu began targeting the stolen jewel as well as the Priestess of Light, who was living in a hidden village. The Kimon were working behind the scenes to bring about a revival of the Toyotomi. What is their intent? As the mystery deepens, the grand battle between the Hiruko and the Kimon over the treasure begins.
In that battle, there was a man who came in from rather unusual circumstances. His name: Kibagami Jubei. Having the ability to defeat enemies by using the art of Shippuu no Iai to create kamaitachi, he is a highly skilled "Ninja for Hire." Claiming he was just angry that they were disturbing his sleep, Jubei refuses to get involved in the fighting any further, but as fate would have it, he and the jewel and the Priestess of Light are brought together. Perhaps by coincidence or perhaps he was called by something, but in the hidden village he entered was the Priestess of Light, Shigure. The hidden village is destroyed in an attack by the Kimon Shu. Along with the aged ninja Dakuan and the boy ninja Tsubute who helped Shigure when she was being pursued, Jubei is pulled into the journey to protect Shigure. Having been told by Dakuan that she seems to have some connection with the Yagyuu Clan, Shigure sets off for the Yagyuu village, wanting to know the secrets of her own birth. The path is littered with the persistently pursuing Hiruko Ninja and Kimon Shu. One after the other, Jubei's Shippuu no Tachi cuts down the unearthly youjutsu that come after them.
Calling this violent battle to the death, what is the true power of the jewel and the Priestess of Light..!?