In an unnamed Japanese school, a hierarchy of supernatural beings called yokai exists, each one tied to one of the Seven Mysteries of the school. These yokai are locked in a constant struggle for territory and power, claiming ownership of specific urban legends and eliminating anyone who investigates them. The series follows numerous self-contained short stories that explore the theme of bullying, with each protagonist being either a victim or a perpetrator of it.

The central narrative begins with Marie Moriya, a timid student who suffers relentless bullying from her classmates and sexual abuse from her homeroom teacher, Kanamori, in an abandoned school building. Desperate and alone, Marie wishes for revenge, catching the attention of the school's yokai. The third-highest ranking among them, Higanbana, who takes the form of a beautiful Western doll in the infirmary and is known as the Dancing Higanbana, offers Marie the chance to become a new, eighth mystery named Mesomeso, based on the legend of a crying ghost in the toilet. After Kanamori strangles her to death, Marie accepts the offer, becoming a yokai herself.

As Mesomeso, Marie appears throughout the subsequent story arcs, either supporting victims of bullying or confronting the bullies themselves. Higanbana, who treats Marie as her personal assistant, regularly torments cruel or weak-willed students, acting as either an antagonist or an antihero depending on the story. Other notable arcs feature characters such as Takeshi Nonomiya, a member of the journalism club whose past actions of bullying a classmate named Yoko Numata led to her suicide, and Reiko Osumi, a shy girl who becomes the target of bullies and becomes friends with another victim named Yukari Sakaki. The series also includes the Director, the oldest and highest-ranking school yokai, who possesses the ability to erase people's existence from memory, thus covering up the disappearances caused by the other yokai.