Thirty-two years ago, the world was engulfed by overflowing black illusions. Kaoru Tsukimiya, a "Witch Hunter" who hunts down the phantoms emerging from the "Black Paradise" (Kuro-rakuen)—an alternate world threatening human survival—visits "Calamity Dragon Island" (Garyuu-tou) seeking revenge, where he meets Fiona, the "Witch of the White Flower." She, who runs a coffee shop and acts as a "jack-of-all-trades" (almost), makes a proposal to Kaoru: "I want you to be my bodyguard." "...Huh?" Confused yet finding himself living there, Kaoru’s mornings begin. The very next day, a case is brought to "Byouyuukan." The first challenge that the "Witch" and the "Witch Hunter" face is a missing person case occurring at the "Skeletal Pavilion Tower" (Gaikakurou), an ultra-massive, multi-layered structure in Q City.