"Toilet-Bound Hanako-kun" is a supernatural anime series based on the manga by AidaIro. The story is set at Kamome Academy, a school rumored to be haunted by various supernatural entities known as "school mysteries." Among these is Hanako-kun, the seventh and most famous mystery, who is said to haunt the girls' bathroom on the third floor. Hanako-kun is a ghost bound to the school, tasked with maintaining balance between the human and supernatural worlds.

The protagonist, Nene Yashiro, is a first-year high school student with a fascination for the occult and a desire for romance. After summoning Hanako-kun to grant her wish for love, she inadvertently becomes his assistant, bound to help him in his duties. Hanako-kun, despite his mischievous and enigmatic demeanor, is a complex character with a tragic past tied to the school. Together, Nene and Hanako-kun investigate and resolve supernatural occurrences within Kamome Academy, often involving other school mysteries or apparitions.

Key characters include Kou Minamoto, a young exorcist from a family of spiritualists who initially seeks to eliminate Hanako-kun but later becomes an ally. Mitsuba Sousuke, a ghostly figure with ties to Kou, adds emotional depth to the narrative as his story intertwines with the main plot. The series explores themes of life, death, and the lingering regrets of spirits, often blending humor with poignant moments.

The plot delves into the mysteries surrounding Hanako-kun's existence, his connection to the school, and the consequences of tampering with the boundary between worlds. As Nene grows closer to Hanako-kun, she uncovers secrets about his past and the true nature of his role as a school mystery. The series balances episodic supernatural investigations with an overarching narrative, gradually revealing the larger stakes and the intricate relationships between characters. The tone shifts between lighthearted comedy and darker, more introspective moments, creating a dynamic and engaging story.