A high school boy named Kimihiro Watanuki possesses the unwanted ability to see ayakashi, spirits invisible to most people. Plagued by these supernatural visions, he one day finds himself inexplicably drawn into a mysterious shop. Its proprietress is Yuko Ichihara, a powerful and enigmatic witch who has the ability to grant any wish, but always at a price equal to its value. Yuko offers to rid Watanuki of his tormenting spirits. In exchange for this service, he must work in her shop as compensation, performing chores and assisting her with clients who come to have their own wishes granted.

The series is set in a contemporary Japan where the mundane world exists alongside a hidden realm of spirits, curses, and magical contracts. Yuko’s shop exists as a liminal space, accessible only to those who are fated to find it. The central narrative follows Watanuki as he navigates his new, strange occupation. He is a naturally loud and reluctant employee, often reacting with fear and frustration to the bizarre situations Yuko thrusts upon him. Working alongside him are the shop's resident creatures, Maru and Moro, and the ever-cheerful Mokona, a white, rabbit-like being with a large red jewel on its forehead.

Watanuki's life at school is equally complicated by his relationships with two classmates. He harbors an unrequited, intense crush on the sweet and seemingly perfect Himawari Kunogi. His primary rival is the quiet, stoic Shizuka Domeki, an archery club member whom Watanuki constantly berates for his cool demeanor. Despite Watanuki’s hostility, Domeki possesses a unique spiritual power of his own: the ability to repel spirits, which proves invaluable whenever Watanuki finds himself in danger.

Throughout its eight episodes, the series adapts several key story arcs from the original manga. The narrative structure is largely episodic, with each week bringing a new client to the shop who must exchange something precious for their heart's desire. These cases range from retrieving a cursed ring for a woman to confronting a parasitic spirit that feeds on a person's luck. Each case reinforces the law of equivalent exchange, demonstrating that interfering with fate or granting a wish always carries a tangible, and sometimes painful, cost. Watanuki slowly learns the gravity of Yuko’s work and the heavy responsibility of his new job.

A significant recurring threat is the spider demon Jorogumo, who has a past connection to Yuko and a particular interest in Watanuki. The series builds toward a confrontation with her as she seeks to claim Watanuki’s eye, a price that was taken from him in the past. As Watanuki delves deeper into the supernatural world, the cold exterior of Shizuka Domeki proves to be a dependable shield, often putting himself in harm's way to protect Watanuki from physical and spiritual attacks. Meanwhile, Himawari’s cheerful nature is gradually revealed to be a mask for a tragic secret she desperately tries to hide, as she believes she is cursed to bring misfortune to those around her. The series culminates in a resolution that forces Watanuki to understand the nature of his own desires, the bonds he has formed, and the true cost of his wish to be free of spirits.