SPR is asked by a person who comes all the way out from the seaside to solve a dangerous case, of which three psychics have already attempted to solve and died as a result. Naru is possessed by a spirit when Ayako exorcises a strong spirit possessing a member of the family involved. Mai dreams of the history of the spirits, with her teammates assuming roles within the dream, and Naru guiding her to where the spirits have gone.
Madoka, an associate of Naru's, requests the SPR take on a case for the former Prime Minister and investigate the mysterious disappearances of young people at one of his properties. Before the case, Naru asks Yasuhara to pretend to be SPR's director in his stead. The SPR team join two other teams of investigators, one of which requests they all participate in a séance which has an unexpected result.
The highly publicised Ryokuryou High School is brought to the SPR's attention when students report a series of terrifying events, including a ghostly dog attacking them. The SPR gathers information with the help of the school valedictorian, Yasuhara, and learn the incidents began after Sakauchi, a first year student, committed suicide. During the installation of cameras around the school, Mai encounters Sakauchi's ghost.
John brings the SPR their next case on Christmas Eve. Children at a local church are being possessed by the ghost of a mute boy who vanished one day during a game of Hide and Seek. The boy, Kenji, hides in the woods once he claims a body. While in control of a child, he mistakes Lin for his dead father and clings to him. John exorcises Kenji from the child he resides in, but Kenji then promptly possesses Mai.
Masako requests Naru investigate a park where over six months, couples have had water dumped over them from thin air. The team, excluding Lin, split up at Masako's suggestion into pairs and they soon attract the spirit of a woman. Taking possession of Masako's body, the woman explains she died soon after being cheated on by her boyfriend. Mai convinces her to let go and move on to heaven, but not until they have forced the cheating partner to acknowledge the hurt he caused.
The SPR are asked to handle a case at the Yuasa High School, where a series of unusual events are seemingly related to a cursed desk and a haunted clubroom. Rumours circulating the school population implicate a girl with psychokinesis, who had previously vowed to 'curse to death' all the doubters of her gifts.
The SPR team, joined by the exorcists and mediums from the previous case, are requested at a house where poltergeist-like activity has been taking place. Soon after their arrival, the ghostly occurrences escalate, leading Bou-san to conclude the house is haunted by something more than a mere poltergeist. A young girl in the family, Ayami, exhibits strange behavior, claiming her doll Minnie has been speaking to her. The SPR team observe Minnie closely, with disturbing results.
Mai meets Naru while exchanging ghost stories with her friends, and learns her school principal has hired him to investigate an allegedly haunted school building. Mai later causes the injury of Naru's assistant and is forced to stand in as a temporary replacement. The principal also brings in several exorcists and mediums, and more help arrives in the form of a classmate of Mai's, who claims to have the ability to sense spirits.
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.
The anime has already ended its run. Many fans have asked for a second season, but while there has been no firm confirmation, some fans believe there is a possibility of a return to be around 2009. The manga is still ongoing; hence beliefs that there could be a possibility of a second season. The author has been quoted as saying that she is currently working on a girl's horror story that she began years ago (which is assumed to be Ghost Hunt). There is also a possibility that the Ghost Hunt manga will finish after all the storylines in the novels have been finished since Fuyumi Ono stopped writing "Ghost Hunt," the novels, in 1994. Read Article!