The war between the Iga and Sanada ninja clans is heating up, and a prominent gunsmith is on both clan's radar. Shinsuke Kakei, the gunsmith, is essentially a pacifist, but believes his weapons can bring peace to the land if put in the hands of the right group. Kasumi is sent to convince Kakei to come and work for them, and keep the guns out of the hands of the Iga. Of course Hattori, along with his sister Sayuri, have other plans for Kakei and his wife.

The year is 2099, there is tumult everywhere and Japan is dominated by a secretive society. A mysterious girl called Shin roams the country and its outlands. There is an investigation, infiltration, an alliance and a betrayal. What is to become of Japan given its rulers, the outlaw and the Green Turtle?