Basilisk pits the Iga and Kouga ninja clans against each other in a feud that has lasted for centuries. When the warlord Ieyasu Tokugawa orders a ceasefire, the two houses are forced to lay down their arms, but the peace only hides the hatred beneath the surface.
Years later, Gennosuke Kouga, heir to the Kouga clan, and Oboro Iga, heir to the Iga clan, have fallen in love and hope to secure peace through marriage. Their hopes collapse when the rivalry between the clans flares up again and they are drawn into another war. At the center of the conflict is a succession dispute: Ieyasu's two grandsons both claim the right to become the next shogun, and to settle the matter, the Kouga and Iga are each ordered to send their ten best warriors into a bloody battle royale. Two scrolls bearing the fighters' names are handed out and marked in blood whenever a warrior falls, while the winner earns the favor of the Tokugawa shogunate for a thousand years. Torn between their love for each other and their duty to their clans, Gennosuke and Oboro are forced to confront the cost of peace and decide the fate of both houses.