June 1565. Just before dawn, ninja master Hiro Hattori is visited by Kazu, a fellow shinobi working undercover in the shogunate. A few hours earlier, Saburo, the shogun's cousin, was stabbed to death in the shogun's palace. The murder weapon is Kazu's personal dagger. Kazu claims to be innocent and begs Hiro for help, but his past causes Hiro to doubt the young shinobi's words. When the shogun summons Hiro and Father Mateo, a Portuguese Jesuit priest under Hiro's protection, and orders them to find the killer, Hiro is forced to choose between friendship and his own honor. During the investigation, a plan to assassinate the shogun and overthrow the ruling Ashikaga clan is revealed. With Lord Oda's enemy forces approaching Kyoto and an assassin poised to strike again, Hiro must use his skills as an assassin to determine the killer's identity and protect the shogun at all costs. Kazoo, now stranded in the city, still refuses to reveal his location at the time of the murder. But those suspected of being in the shogunate—Saburo's wife and the shogun's chief groom—also have reasons to want Saburo dead. The shogun demands the killer's head before Lord Oda reaches the city. Hiro and Father Mateo must identify the killer... or die in his place.