"Toilet-Bound Hanako-kun" is a supernatural anime series based on the manga by AidaIro. The story is set in Kamome Academy, a school rumored to house seven mysteries, each tied to a supernatural entity. The central mystery revolves around Hanako-kun, the ghost of a young boy who haunts the girls' bathroom on the third floor. According to legend, summoning Hanako-kun grants a wish, but at a cost.

Nene Yashiro, a first-year high school student, summons Hanako-kun out of desperation to fulfill her romantic desires. However, her wish backfires, and she becomes bound to him as his assistant. Hanako-kun, whose real name is Amane Yugi, is a mischievous yet enigmatic ghost tasked with maintaining the balance between the human and supernatural worlds. Together, Nene and Hanako-kun investigate and resolve disturbances caused by other supernatural entities, often tied to the school's seven mysteries.

The series explores the dynamics between Nene and Hanako-kun as they navigate their partnership, uncovering secrets about Hanako-kun's past and the true nature of the school's mysteries. Supporting characters include Kou Minamoto, a young exorcist from a family of spiritual warriors, who becomes an ally and friend to Nene. Kou is determined to uncover the truth about Hanako-kun and his intentions. Other key figures include Mitsuba Sousuke, a ghostly boy with a tragic past, and Tsukasa Yugi, Hanako-kun's mysterious and malevolent twin brother, whose actions often complicate the protagonists' efforts.

The narrative blends humor, mystery, and emotional depth, delving into themes of regret, redemption, and the consequences of wishes. Each arc focuses on resolving conflicts tied to the supernatural entities, while gradually revealing the backstories of the main characters and the darker truths behind the school's legends. The series maintains a balance between lighthearted moments and darker, more poignant undertones, creating a compelling and multifaceted story.