"Toilet-Bound Hanako-kun" is a supernatural manga series set in Kamome Academy, a school rumored to be haunted by various spirits. The story centers on Nene Yashiro, a first-year high school student fascinated by the occult. She becomes entangled with Hanako-kun, the ghost of a boy who haunts the girls' bathroom and is said to grant wishes in exchange for a price. Hanako-kun is revealed to be the seventh and most powerful of the school's Seven Mysteries, supernatural beings tied to specific locations and legends within the academy.

Nene's initial wish to Hanako-kun is to find love, but her wish backfires, leading to her transformation into a fish. To reverse this, she forms a contract with Hanako-kun, becoming his assistant in maintaining the balance between the human and supernatural worlds. Together, they investigate and resolve disturbances caused by other apparitions, often involving the other Seven Mysteries or supernatural entities that threaten the school.

The narrative explores themes of boundaries, identity, and the consequences of desires. Hanako-kun, despite his mischievous demeanor, harbors a tragic past tied to his death and his role as a supernatural guardian. Nene, while initially naive and driven by romantic fantasies, grows more resilient and resourceful as she navigates the dangers of the spirit world. The dynamic between Nene and Hanako-kun evolves from a reluctant partnership to a deep, mutual bond, though their relationship is complicated by Hanako-kun's mysterious past and his duties as a supernatural entity.

Other key characters include Kou Minamoto, a young exorcist from a family of spiritual warriors who initially seeks to eliminate Hanako-kun but later becomes an ally. Kou's interactions with Nene and Hanako-kun add layers of conflict and camaraderie, as he grapples with his family's expectations and his own moral compass. Additionally, the series introduces other members of the Seven Mysteries, each with their own unique abilities and backstories, further enriching the supernatural lore of Kamome Academy.

The plot intertwines episodic supernatural investigations with an overarching narrative that delves into the origins of Hanako-kun and the true nature of the Seven Mysteries. As the story progresses, darker secrets about the academy, its connection to the supernatural, and the fates of those who interact with the spirits are revealed. The series balances humor, mystery, and emotional depth, creating a compelling exploration of the human and supernatural worlds colliding within the confines of Kamome Academy.