"Kuro Nyago" centers on a mysterious black cat named Nyago, who possesses the ability to transform into a human-like form. The narrative unfolds in a small, rural town where supernatural occurrences are commonplace, yet often hidden from the human population. Nyago, while appearing as an ordinary cat to most, interacts with a select group of individuals who can perceive his true nature. These individuals include a young girl named Hana, who discovers Nyago's secret after rescuing him from a storm, and an elderly shopkeeper, Mr. Takeda, who serves as a mentor figure with knowledge of the town's supernatural history.

The plot revolves around Nyago's efforts to protect the town from malevolent spirits and otherworldly threats that emerge from a nearby forest. These entities are drawn to the town due to an ancient artifact hidden within its boundaries, which holds immense power. Nyago, bound by a centuries-old pact, must balance his duty to safeguard the artifact with his growing attachment to Hana and the townspeople. As the story progresses, Nyago's past is gradually revealed, including his origins as a guardian spirit and the tragic events that led to his current form.

Key characters include Hana, whose curiosity and bravery often place her at the center of conflicts; Mr. Takeda, who provides guidance and historical context; and a rival spirit named Shiro, a white cat with a contrasting personality and conflicting motives. Shiro's presence introduces tension, as their shared history and differing philosophies on humanity create a dynamic interplay. The series explores themes of loyalty, sacrifice, and the coexistence of humans and spirits, with each episode advancing the overarching mystery of the artifact and its connection to the town's fate.

The narrative structure blends episodic adventures with an overarching plot, allowing for character development and world-building. The town itself serves as a character, with its folklore and traditions playing a significant role in the story. The series maintains a balance between lighthearted moments and darker, more suspenseful elements, creating a tone that appeals to a wide audience. Through its exploration of supernatural elements and human relationships, "Kuro Nyago" offers a compelling and cohesive storyline.