The story takes place in the year 1614. Two ninja clans, Tsubagakure of the Iga and Manjidani of Kouga, battle each other to determine which grandson of Tokugawa Ieyasu will become the next shogun. The deadly competition between 10 elite ninja from each clan unleashes a centuries-old hatred that threatens to destroy all hope for peace between them.

At the dawn of Japan's Azuchi-Momoyama period (the late 16th century) two rival clan of Ninja, the Iga Tsubagakure and Kouga Manjidani, are engaged in a bitter blood feud that has spanned for centuries. The fighting finally ends when Hattori Hanzo the 1st succeeds in forging a cease fire between the two clans by conscripting both into the service of Tokugawa Ieyasu (the man who seized power to become Shogun and form Japan's first truly stable form of centralized government). Regardless, hostilities and bad blood remain between Kouga and Iga, ensuring a tenuous co-existence at best.

Fast forward to the year 1614; Ieyasu has retired from power (although he still wields considerable influence within the government) and passed the torch to his son Hidetada. Unfortunately, a succession dispute has risen concerning which of Ieyasu's grandsons are destined to take up the reins of power when their father finally decides to step down. The various government retainers are beginning to take sides and the Tokugawa Shogunate is on the verge of tearing itself apart.

In order to solve the problem before it spirals out of control, Ieyasu orders the no hostilities pact between Kouga and Iga canceled and promptly commands each clan to send 10 of their best ninja to enter a ruthless and bloody competition of kill or be killed. The leaders of the two clans kill each other off outside of the walls of the palace, leaving nine ninjas in each side to determine the outcome of the battle. Having received a scroll considerably early, the Iga gain the advantage and quickly kill four more of the Kouga before they even become aware the pact has been breached. However, upon the discovery of the pact's ending the Kouga soon retaliate, killing almost all of the Iga, and forcing the new young leaders into a path that will test the true strength of their love. Prior to the conflicts renewal, Kouga and Iga's two young heirs (Gennosuke and Oboro respectively) were betrothed to each other in the hopes that their union would finally dispel their clan's long-seated animosity toward each other. Forced headlong onto separate sides of a conflict they want no part of, Gennosuke and Oboro must now choose whether to kill the person they love or lead their entire clan to annihilation. Against centuries of old hatred and the horrors of war, is love even capable of surviving? Each clan will represent one of the two factions supporting Ieyasu's grandsons; the names of their selected fighters recorded on two identical scrolls to be marked out in blood upon their death. The clan that slays the chosen ten of the other will be given favor for a thousand years while the grandson they represent will be pronounced the undisputed heir to the Shogunate.

Basilisk (バジリスク〜甲賀忍法帖〜 Bajirisuku ~Kōga Ninpō Chō~, Basilisk: The Kōga Ninja Scrolls) is a Japanese manga and anime series. The manga was written and illustrated by Masaki Segawa and published in Japan in 2003 and 2004, based on the novel The Kouga Ninja Scrolls by Futaro Yamada published in 1958. The anime, produced in 2005 by Gonzo Studios, closely follows the manga aside from a handful of distinctions. The manga won the 2004 Kodansha Manga Award for general manga. The manga was later followed by a sequel series titled The Yagyu Ninja Scrolls which was also based on a novel by Futaro Yamada.