Koga Michiru arrives at his new academy — built deep in the mountains around a notably large clock tower — and manages to break an expensive statue on his very first day. As punishment, he is assigned to the Bureau for the Investigation of Special Affairs alongside the other student responsible for the incident. The Bureau is headquartered in the academy's underground library, and the girl waiting for them there explains the situation flatly: magic exists in this school. When the clock tower chimes, the Realm of Night appears and merges with the building. Their job is to handle what comes through. A Clockwork Ley-Line follows Koga as he learns to deal with the supernatural Mists while navigating the relationships that form inside the Bureau.