The famous Seven Mysteries that every school seems to have are a staple of Japanese urban legends. One of the most well-known of these tales is that of Hanako-san: the ghost of a young girl who haunts the school's bathrooms. Kamome Academy has its own version of Hanako-san's legend. Rumors claim that if one successfully manages to summon Hanako-san, she will grant her summoner any wish. Lured by the gossip, many people have tried to call upon her, yet every attempt has failed. However, when Nene Yashiro, a girl hoping for romantic fortune, dares to summon Hanako-san, she discovers that the rumored "girl" is actually a boy! After a series of unfortunate events involving Yashiro's romantic desires, she is unwillingly entangled in the world of the supernatural, becoming Hanako-kun's assistant. Soon, she finds out about Hanako-kun's lesser-known duty: maintaining the fragile balance between mortals and apparitions.

There is a rumor in Kamome Academy that somewhere within the school premises lies a clock that governs the passage of time in the academy. That clock is overseen by three clock keepers—each representing the past, present, and future. Despite this, an unforeseen event causes mayhem, with students rapidly aging and the academy's infrastructure falling apart. Nene Yashiro and Kou Minamoto seek help from Hanako-kun, embarking on a new adventure to find those responsible for this mess. However, what they uncover is more than just the culprits' identity. As hidden truths are revealed and new vows are established, the academy students and its apparitions find themselves in a game of fate, where the living fight to free themselves from its grasp.