"Mononote - Edo Shinobi Kagyō" is set in the Edo period of Japan, blending historical elements with supernatural intrigue. The narrative centers on a secretive ninja clan known as the Mononote, who operate in the shadows of Edo society. The clan specializes in combating malevolent spirits and supernatural threats that plague the city, using a combination of traditional ninja skills and mystical techniques. Their mission is to maintain balance and protect the populace from unseen dangers, all while remaining hidden from the public eye.

The protagonist, Kurogumo, is a skilled and stoic ninja of the Mononote clan. He is tasked with investigating a series of mysterious incidents involving vengeful spirits and cursed artifacts. As Kurogumo delves deeper into these cases, he uncovers a larger conspiracy that threatens not only Edo but the entire fabric of the spiritual world. Alongside him is a diverse cast of characters, including fellow clan members, each with unique abilities and personal motivations. These allies and rivals add depth to the story, as their interactions and conflicts shape the unfolding events.

The plot is driven by episodic investigations, with each arc focusing on a specific supernatural threat or cursed object. These individual stories are interconnected, gradually revealing the overarching conspiracy tied to a powerful and ancient entity seeking to disrupt the balance between the human and spirit realms. The narrative explores themes of duty, sacrifice, and the moral complexities of wielding power in a world where the line between good and evil is often blurred.

The setting of Edo is richly depicted, with attention to historical detail and atmospheric elements that enhance the supernatural tone. The interplay between the human and spirit worlds is a central aspect of the story, with the Mononote clan serving as mediators between these realms. The manga balances action, mystery, and character development, creating a compelling narrative that appeals to fans of historical fiction and supernatural genres.