Oboro (Yukie Nakama), a granddaughter of Ogen (Riri), is the matriarch of the Iga clan. She meets and falls in love with Gennosuke, the son of Danjo Koga (Minoru Terada), the leader of the Koga clan. Living in the remote mountains, these two clans have, over the centuries, perfected the arts of ninjutsu (known as "Shinobi"), which is far beyond the reach of mere mortals. They are also ancestral rivals and, under the order of Hanzo Hattori (Yutaka Matsushige), chief ninja to Shogun Tokugawa Ieyasu, are forbidden to exchange secret techniques.

Seeking to consolidate Tokugawa rule and seeing the two clans as a threat to it, a powerful Tendai priest and Tokugawa adviser, Nankobo Tenkai (Renji Ishibashi), schemes to set them against each other. He commands the two clans to each choose five champions who will battle to the death. The survivor will be elevated in rank and power.

Both Oboro and Gennosuke are selected as champions, but neither are aware, at least initially, of each other's position. Also, Gennosuke doubts the shogunate's good intentions and refuses to take part in the contest. But when his comrades begin to fall, he is forced into action. He cannot, however, bring himself to battle at least one Iga warrior: Oboro...