Kyoichi Utsume and his younger brother Souji were captured by a kami-kakushi, a mysterious spirit that spirits people away to another world, when they were children. Kyoichi somehow returned, but his brother never did. This traumatic event left Kyoichi with the ability to sense the other world and an immense, morbid knowledge of the occult. Now a high school student, he is a notorious loner, always dressed in black, emotionless, and secretly longing for death. He rejects the concept of love and is known ominously as the Dark Lord.

The story begins at Seisou Academy, where Utsume is a member of the literature club alongside his few friends. The club includes the athletic and protective Toshiya Murakami, the sharp-tongued and proud Aki Kidono, the very ordinary but loyal Takemi Kondou, and the kind-hearted Ryoko Kusakabe. One day, Utsume surprises everyone by introducing a new girlfriend named Ayame, a fragile and beautiful girl with a lonely smile who is strangely easy to overlook. Shortly after this introduction, Utsume and Ayame vanish completely.

The remaining members of the literature club discover that Ayame is a kami-kakushi, a being from the other world who has gone mad from loneliness. She has drawn Utsume back to that realm, and he may not wish to return. To rescue their friend, the group splits up to seek answers. They consult a mysterious figure known as Jinno Kageyuki, a being who may have once been human but has become magic itself. They also encounter agents of The Agency, a secret government organization whose mission is to combat the other world and suppress public knowledge of the supernatural. The Agency considers Utsume an experiment and is willing to erase the memories of those involved. The first volume, Spirited Away, follows their desperate and dangerous attempt to retrieve Utsume from the other world.

The series spans thirteen volumes, with each installment presenting a new supernatural case linked by the ongoing struggle between the human world and the other world. Subsequent narrative arcs include a cursed fax that haunts Aki with invisible dogs, a student suffering from nightmares connected to a famous occultist, and a ouija board session that summons a ghostly child. The group repeatedly encounters otherworldly threats such as cursed mirrors, sacrificial ghosts, and house spirits, all while navigating their complex relationships and personal traumas. The central conflict often involves The Agency's cold, scientific methods clashing with the personal, emotional stakes of the students, who are willing to risk their lives for each other.