In a Roman Catholic convent in Montreal, Quebec, the quiet of evening prayers is shattered when screams erupt from the room of Sister Agnes, Meg Tilly, a young novice. Agnes is found in her room bleeding, and in a basket lies a dead infant. The stark discovery sets off a chain of questions about what really happened in the confinement of the convent, where devotion and fear mingle in the dim corridors.
Sister Agnes is charged with manslaughter, and the case lands on the desk of the court psychiatrist Dr. Martha Livingston, Jane Fonda. Her mission is to determine whether Agnes is competent to stand trial. In their early interviews, Agnes claims she does not remember being pregnant or giving birth, and she reveals a startling limited understanding of how babies are conceived. Mother Superior Miriam, Anne Bancroft, the head of the convent, describes her as an “innocent” who has been kept sheltered from the world, insisting that Agnes could not have known what pregnancy was or who the father might be. The tension between protecting Agnes and uncovering the truth becomes a central drama of the investigation.
Mother Miriam recaps a troubling episode: Agnes stopped eating because she believed she was getting fat, then displayed stigmata on her hand that healed itself within a day. Agnes recounts a growing closeness with Sister Marie-Paul, the eldest nun, who supposedly shows her a "secret place"—a bell tower—that she later leads Livingston to see. The two women spar over family history, Agnes’s mother, and how much Agnes truly understands about sex and birth, underscoring a theme of naivety versus exposure to the world beyond the cloister.
Miriam insists that Agnes must have conceived on January 23, the night she burned her bedsheets and confessed they were “stained.” While the court’s gaze wanders across the convent grounds, Livingston discovers a barn off the property. A brief clash with a young Monsignor raises questions about faith, doubt, and the ability of a medical professional to treat Agnes with dignity when her beliefs are in conflict with reason. Livingston learns that Agnes’s mother suffered verbal and sexual abuse, and that Agnes is Miriam’s niece, a revelation that deepens the complicated web of loyalty, guilt, and family ties within the convent walls.
Permission to hypnotize Agnes is granted, but Miriam resists, fearing that such an intervention would strip away the girl’s innocence. Under hypnosis, Agnes admits she gave birth and that another nun knew about the pregnancy, though she refuses to identify the accomplice. A workroom in the convent hides a concealed staircase that leads to a tunnel opening into the barn, a detail an archivist explains is common in older convents to allow discreet movement between buildings during harsh winters. The conflict over the investigation intensifies as Miriam seeks to have Livingston removed; the court, however, keeps the doctor on the case.
A second round of hypnosis brings more dramatic revelations. Miriam acknowledges that she knew about the pregnancy and had placed the wastebasket in Agnes’s room, yet she continues to deny any role in the baby’s death. Under trance, Agnes recalls that on the night Sister Marie-Paul died, she was told by someone who had seen “Him” from the bell tower to meet “Him” in the barn. The recovered memories hint at a presence—human or divine—that overshadows the event. Then, suddenly, Agnes presents the stigmata again and bleeds, declaring that “He” raped her and that she hates God for it. The record indicates that Miriam was present at the birth but left briefly, and Agnes believes the baby was killed because it was a "mistake" like herself.
The trial culminates in a verdict of not guilty by reason of insanity, and Agnes is returned to the convent, where she will be visited by a doctor periodically. Before the judge, she reveals one final, haunting detail: she heard “Him” singing beneath her bedroom window for six nights in a row, and on the seventh night, he lay on top of her, implying that she may have been raped and impregnated by a trespasser. The case leaves open the possibility of further inquiries into faith, memory, and the marks left by trauma on a young woman who remains within the walls she knows as home.
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