The story of Shabake takes place during the Edo period in Nihonbashi, where Ichitaro is the sickly young heir to Nagasakiya, one of the area’s largest and most prominent stores. Due to his extremely frail constitution, he is largely confined to his home and unable to venture out into the city. Despite his human frailty, Ichitaro has grown up surrounded by the supernatural; he is constantly protected and served by various ayakashi, including the loyal Shirasa wa and the dog-like Inugami who act as his devoted attendants.

One night, Ichitaro defies his family's overprotective rules and sneaks out into the city. During this secret excursion, he becomes the sole witness to a brutal murder. From that day forward, a string of bizarre and unexplainable killings plagues Edo, and Ichitaro finds himself inexplicably linked to the unfolding violence. Unable to ignore the danger or rely on his own physical strength, Ichitaro decides to investigate the crimes with the help of his ayakashi companions, who act as his hands and eyes on the dangerous streets.

The series follows Ichitaro as he uses his wits and the abilities of his supernatural friends to solve these dark mysteries. The narrative blends the detective genre with historical fantasy, creating a world where humans and spirits coexist, though most ordinary people remain unaware of the ayakashi living beside them. As the bizarre cases progress, Ichitaro discovers that the secrets behind the murders are tied to his own past and the very nature of his existence, forcing him to confront a terrifying truth that his loyal protectors have been trying to hide from him. A key narrative arc involves Ichitaro pursuing a mysterious tsukumogami, a spirit born from an old tool, which is possessing people across the city and driving them to madness in its desperate search for a medicine that can grant it true life. This investigation brings him into direct conflict with a dark reflection of his own struggle against a frail body and the fear of death, forcing his ayakashi friends to act as his defenders in a climactic confrontation that ultimately gives Ichitaro a newfound hope and a determined will to live.