"Ninja Resurrection" is a dark and violent anime series that draws inspiration from historical events and folklore, blending them with supernatural elements. The narrative is set in 17th-century Japan during the Shimabara Rebellion, a period marked by peasant uprisings and religious persecution. The story centers on Jubei Yagyu, a skilled and morally ambiguous swordsman, who becomes entangled in a conflict involving a mysterious figure claiming to be the reincarnation of Jesus Christ. This figure, Shiro Amakusa, leads a group of oppressed Christians in a revolt against the Tokugawa shogunate, promising salvation through his divine powers.

As the rebellion gains momentum, Jubei is reluctantly drawn into the chaos. Shiro's followers, driven by desperation and faith, begin to exhibit supernatural abilities, transforming into monstrous beings. These transformations are tied to Shiro's dark powers, which blur the line between divine intervention and demonic influence. Jubei, while initially indifferent to the political and religious strife, is compelled to confront Shiro after witnessing the devastation wrought by his followers. The series explores themes of faith, power, and the consequences of blind devotion, as Jubei navigates a morally complex landscape where the lines between hero and villain are often blurred.

The supporting cast includes historical and fictional characters, such as the loyal samurai and government agents tasked with quelling the rebellion. These characters provide additional perspectives on the conflict, highlighting the tension between duty, honor, and personal beliefs. The series is notable for its graphic depictions of violence and its exploration of the darker aspects of human nature, as characters grapple with their own motivations and the consequences of their actions. The narrative builds toward a climactic confrontation between Jubei and Shiro, culminating in a battle that questions the nature of divinity and the cost of wielding power.