"Ninja Scroll" is set in feudal Japan and centers on Jubei Kibagami, a wandering swordsman with exceptional skill. Jubei becomes entangled in a dangerous conspiracy when he encounters Kagero, a kunoichi (female ninja) from the Koga clan, who is being pursued by the Eight Devils of Kimon, a group of supernatural assassins. The Devils serve under Genma, a power-hungry warlord seeking to overthrow the Tokugawa shogunate using a secret cache of gold. Jubei reluctantly agrees to assist Kagero and Dakuan, a cunning government spy, in thwarting Genma's plans.

The narrative unfolds as Jubei and his allies face off against the Eight Devils, each possessing unique and deadly abilities rooted in dark sorcery or advanced ninja techniques. Kagero, who is immune to poison due to her training, becomes a key asset in their mission, though her tragic past and vulnerability add depth to her character. Dakuan, while morally ambiguous, provides strategic guidance and manipulates events to ensure the shogunate's survival.

As the story progresses, Jubei confronts his own moral dilemmas and past, particularly his connection to the Devils and his reluctance to be drawn into political conflicts. The battles are intense and often gruesome, showcasing the brutal realities of ninja warfare and the supernatural elements that define the series. The climax involves a final confrontation with Genma, revealing the extent of his ambitions and the true nature of the Devils' powers.

Themes of loyalty, betrayal, and the cost of power permeate the narrative, with Jubei's journey serving as the focal point. The series blends historical elements with fantastical storytelling, creating a dark and immersive world. The characters are complex, with their motivations and relationships driving the plot forward. "Ninja Scroll" is notable for its intricate fight sequences, morally gray characters, and a plot that balances action with deeper thematic exploration.