"Hanako @ Lavatory" is a supernatural romance manga series set in Kamome Academy, a school rumored to be haunted by seven mysteries, each tied to a specific location on campus. The story centers on Nene Yashiro, a first-year high school student who is deeply fascinated by the occult and romantic fantasies. Desperate to find love, she summons the seventh and most famous mystery, Hanako-san of the Toilet, a ghost said to reside in the girls' bathroom on the third floor of the old school building. Contrary to the eerie legends, Hanako-san, whose real name is Amane Yugi, appears as a mischievous but kind-hearted boy with a checkered past.

Nene forms a contract with Hanene, agreeing to assist him in maintaining the balance between the human and supernatural worlds in exchange for granting her romantic wish. As the series progresses, Nene becomes entangled in the affairs of the other school mysteries, each of which harbors its own secrets and emotional struggles. The narrative explores themes of love, loss, and redemption, delving into the backstories of both the human and supernatural characters. Key figures include Kou Minamoto, a young exorcist from a family of supernatural hunters who becomes Nene's ally, and Mitsuba Sousuke, a ghost with a complicated connection to Kou.

The plot intertwines episodic adventures with an overarching mystery surrounding Hanako's past and the true nature of the school's seven wonders. Nene's relationship with Hanako evolves from a transactional partnership to a deeper emotional bond, complicated by the boundaries between life and death. The series balances humor, romance, and darker, more poignant moments, creating a multifaceted narrative that appeals to fans of both supernatural and emotional storytelling.