The film opens with a priest, Stanley, murdering his wife and asking the town physician to cover up the crime. Three years later, in 1938, Marianne and her husband Linus, a reverend, have moved into Morley Rectory with their daughter Adelaide, tasked by Bishop Malachi with restoring the town's sagging faith. The couple has a strained relationship due to Linus's belief that having sex for pleasure is a sin, as well as his jealous fear that Marianne will cheat on him. These fears are exacerbated by the appearance of Harry Reed, who tells him about the rectory's past and that Stanley's wife strayed, as the rectory made her grow wanton. Bishop Malachi later tries to make Harry leave, only for the man to claim that Bishop Malachi is using the family to fulfill a secret, evil purpose for his Nazi cohorts. Harry is later beaten by some of Bishop Malachi's associates.Marianne is encouraged to meet with Harry at the urging of her deaf housekeeper Betsy. Harry warns her that her lies of Adelaide being her dead sister's child will weaken her to evil forces, as she actually had the child out of wedlock. Marianne is further warned that the rectory will turn people against one another, so the family should leave for their own safety. Back at the house, Linus also experiences a supernatural vision of Marianne committing adultery. This prompts a jealous argument between him and Marianne once she returns, particularly after he discovers that she has been to see Harry. The following day, Marianne receives a visit from Bishop Malachi after a church service. He reveals his knowledge that Adelaide is actually illegitimate and not Linus's child, as well as that the child had been briefly taken away from her while she was in a mental hospital. He orchestrated the child's return and her meeting with Linus, threatening to use his power to take everything away from her if she were to try to leave Morley Hall.Marianne's relationship with Adelaide grows increasingly sour, as the child has begun to talk to an unseen figure she claims is her real mother. Adelaide then goes missing. Marianne unsuccessfully tries to seek help from a drunk Linus before approaching Harry, who agrees to help her. When they return they find that Betsy has been murdered by the now-possessed Linus who is in a trance. Harry is able to draw him out and explains that Adelaide has been abducted by the spirit of a pregnant woman who was murdered by several monks, as she was carrying their child. He then has Linus perform a ritual to help Marianne retrieve Adelaide and confront the spirits haunting the rectory. Marianne is forced to experience nightmarish visions, some of which are related to her past, during which she proclaims that she is unashamed of what she has done. She manages to find and retrieve Adelaide, promising the murdered woman that they will give her and the unborn child a proper burial. They make good on their promise, however Bishop Malachi is shown at some later point digging up the bodies and delivering them to Nazi officials in Stuttgart.