In Jibaku Shounen Hanako-kun, the Seven Mysteries that haunt Kamome Academy turn school gossip into real danger, and none is more famous than Hanako-san, the ghost said to dwell in the girls' bathroom. The legend promises that anyone who successfully summons her can have a wish granted, so rumors keep drawing curious students and desperate believers to the academy's hidden corners.
Nene Yashiro, hoping for romantic fortune, decides to test the story for herself. Instead of the girl she expected, she meets Hanako-kun, a boy spirit bound to the bathroom and to the strange rules governing the academy's supernatural world. After a string of unfortunate events tied to her wish, Nene is dragged into that world and becomes Hanako-kun's assistant.
As the two work together, Nene learns that Hanako-kun has a lesser-known duty: keeping the fragile balance between mortals and apparitions. Between haunted legends, uneasy alliances, and the secrets of Kamome Academy, their bond grows into the heart of the story.