Autumn, 1565: After fleeing Kyoto, master ninja Hiro Hattori and Portuguese Jesuit Father Mateo take refuge with Hiro's ninja clan in the mountains of Iga province. But when an ambassador from the rival Koga clan is murdered during peace negotiations, Hiro and Father Mateo must find the killer in time to prevent a war between the ninja clans. With every suspect a trained assassin, and the evidence incriminating not only Hiro's commander, the infamous ninja Hattori Hanzo, but also Hiro's mother and his former lover, the detectives must struggle to find the truth in a village where deceit is a cultivated art. As tensions rise, the killer strikes again, and Hiro finds himself forced to choose between his family and his honor.