Shinobi centers on the drama resulting from the war between two ninja clans in the early part of the Tokugawa era. In the film, Nakama Yukie portrays Oboro, the granddaughter of Ogen (Lily), the respected Iga clan matriarch, while Odagiri Jo plays Gennosuke, the son of Danjo Koga (Minoru Terada), the powerful Koga clan leader. While living deep within the mountains, the two ninja clans have honed their skills to superhuman levels. Unfortunately, the clans do not get along and are forbidden by imperial decree from sharing their techniques with each other. Viewing the two ninja clans as a threat to his scheme for total domination, the nefarious Nankobo Tenkai (Ishibashi Renji) plots to intensify the rivalry between the two clans. Nakobo creates a contest in which the clans are forced to choose five of their best warriors to participate. The battle, however, isn't just a friendly contest - it's a duel to the death!