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Ghost Hunt follows the adventures of Kazuya Shibuya, the president of the Shibuya Psychic Research Center (SPR) and Mai Taniyama, a first year high school student. The story begins during an exchange of ghost stories between Mai and her friends, who are interrupted twice: first by a mysterious "male student" and then by a fellow classmate, who warns them of how their ghost stories attract spirits.

While out walking, Mai sees the building that all the ghost stories surround and decides to go in. As she is about to touch a camera in the middle of the room, a man stops her and ends up injuring himself. Mai is then forced to work as a stand-in assistant for the man, an employee of the "male student," who was hired to study the "paranormal" events occurring at the school. Mai nicknames this "student" "Naru" for his narcissistic attitude. Naru owns a paranormal investigation company SPR and Mai eventually earns a part-time job at SPR after assisting with the first case. The more involved Mai becomes with Naru, the more she learns about herself and her feelings towards him.

Along with Shibuya's assistant, Lin, the SPR also finds itself assisted by various spirit mediums and exorcists.