The focus of Haunted Junction is Saitou High School, where both students and spirits coexist. The Student Council, made up of three members: Haruto Houjou, a diligent student brought up by a Christian pastor; Kazumi Ryuudou, a young man with an obsession for girls brought up by a Buddhist monk, and Mutsuki Asahina, daughter of a Shinto priest with a liking for young boys, ensures the smooth running of the school for everyone. Although some spirits dwelling the school premises are amiable, others are not. To eliminate malevolent spirits and perilous demons, the Council enlists seven distinctive spirits within the school that Haruto holds seven unique badges for, with each spirit based on common myths and ghost stories in Japanese schools.