"Ninku Knife no Bohyō" is a short anime series that serves as a spin-off of the original "Ninku" manga and anime. The story is set in a world where ninja clans possess unique abilities known as "Ninku," which combine martial arts with supernatural powers. The narrative centers on a young boy named Knife, who becomes entangled in a conflict involving the remnants of the Ninku clans and a mysterious organization seeking to exploit their powers.

Knife, the protagonist, is an orphan with a tragic past, having lost his family to the ongoing strife between the Ninku clans. He is discovered by a wandering swordsman named Fuusuke, who takes him under his wing and trains him in the ways of Ninku. Fuusuke is a former member of the Ninku clans, now living as a drifter, and his motivations for helping Knife are initially unclear. As the story progresses, it is revealed that Fuusuke has a personal vendetta against the organization targeting the Ninku clans, and he sees potential in Knife to help him achieve his goals.

The antagonist organization, led by a shadowy figure known only as "The Boss," seeks to harness the power of Ninku for their own nefarious purposes. They employ a variety of skilled fighters, each with their own unique Ninku abilities, to hunt down and capture or eliminate the remaining Ninku practitioners. This sets the stage for a series of battles and confrontations, as Knife and Fuusuke are forced to confront these enemies while uncovering the truth behind the organization's plans.

Throughout the series, Knife undergoes significant character development, transitioning from a naive and vulnerable child to a determined and capable fighter. His growth is paralleled by the deepening bond between him and Fuusuke, whose gruff exterior hides a deep sense of responsibility and care for his young charge. The dynamic between the two characters is a central focus of the narrative, with their interactions providing both emotional depth and moments of levity amidst the action.

The plot is driven by a combination of episodic battles and overarching storylines, with each encounter revealing more about the world of Ninku and the characters' backstories. The series explores themes of loyalty, revenge, and the cost of power, as Knife and Fuusuke navigate a morally complex landscape where allies and enemies are not always clearly defined. The conclusion ties together the various threads of the story, resolving the immediate conflict while leaving room for further exploration of the Ninku universe.