Haunted Junction centers on Saitou High School—a place where both students and spirits roam the halls—and the Student Council that strives to keep things running smoothly for everyone: Haruto Houjou, the studious son of a Christian pastor; Kazumi Ryuudou, the girl-crazy son of a Buddhist monk; and Mutsuki Asahina, the daughter of a Shinto priest with a thing for boys (that are half her age). Although many of the spirits occupying the halls—and depths—of Saitou are good-natured, there are many that aren't. To rid the school of its evil spirits and dangerous demons, the Student Council employs the help of seven distinct spirits within the school (each based on common myths and ghost stories in Japanese schools) that can be summoned by using seven special badges held by Haruto.