"Basilisk" is a historical fantasy manga set in early 17th-century Japan, during the Edo period. The story revolves around a deadly conflict between two rival ninja clans, the Iga and the Kouga, who have been locked in a bitter feud for centuries. The shogunate, seeking to determine the successor to the aging shogun Tokugawa Ieyasu, orchestrates a brutal competition between the clans. Each clan selects ten of their most skilled ninja to engage in a battle to the death, with the victor deciding the next shogun.

The Iga clan is led by Oboro, the granddaughter of the clan leader, who possesses a unique ability to nullify the supernatural powers of others with her gaze. Despite her pacifist nature, she is thrust into the conflict. The Kouga clan is represented by Gennosuke, Oboro's lover and the grandson of the Kouga leader. Gennosuke wields the "Dojutsu," a powerful eye technique that allows him to manipulate others' perceptions. Their love story becomes a tragic focal point as they are forced to confront each other in the deadly competition.

The narrative unfolds through a series of intense battles, with each ninja showcasing their unique and often supernatural abilities. The Iga and Kouga fighters employ a wide range of techniques, from poison manipulation and shape-shifting to enhanced physical prowess and illusion casting. As the conflict progresses, alliances shift, betrayals occur, and the body count rises, highlighting the brutal nature of the feud and the personal sacrifices made by the characters.

Themes of loyalty, honor, and the devastating consequences of war are central to the story. The manga explores the tension between duty and personal desires, particularly through the relationship between Oboro and Gennosuke, who struggle to reconcile their love with their obligations to their respective clans. The shogunate's manipulation of the clans serves as a critique of political power and its exploitation of human lives for strategic gain.

The artwork complements the dark and violent tone of the narrative, with detailed depictions of the ninja's abilities and the gruesome outcomes of their battles. The historical setting is meticulously rendered, immersing readers in the feudal Japanese backdrop while incorporating fantastical elements that enhance the story's dramatic tension. "Basilisk" is a gripping tale of love, conflict, and the tragic consequences of entrenched rivalries.