At a rural Canadian convent of Les Petites Soeurs de Marie Madeline, screams awaken the resident nuns, who discover their young novice, Sister Agnes, covered in blood. As Agnes is rushed to the hospital, Mother Miriam Ruth uncovers a strangled infant inside the young woman’s wastepaper basket. Sometime later in Montreal, Quebec, psychiatrist Doctor Martha Livingston arrives at city hall as Agnes, Mother Miriam, and another nun leave the courthouse, pursued by television reporters. Inside, court justices ask Martha to examine Agnes and diagnose her insane, so the nun will not be found guilty of manslaughter, and Martha reluctantly takes the case. At the convent, Martha meets with Mother Miriam, who lights the doctor’s cigarette and confesses to being a former smoker. Mother Miriam explains that Agnes’s pregnancy was a mystery to the nuns, and Agnes had contact with only one man, Father Martineau, an elderly gentleman incapable of procreation. Noting her lack of faith in psychiatry, and her desire to protect Agnes’s innocence, Mother Miriam walks away. Martha visits Agnes in her quarters, where the girl sings in religious ecstasy. Agnes remembers being sick the night of the birth, but insists that the other nuns invented the story of the baby. Tired of answering questions, Agnes intends to leave, but returns when Martha offers to be the subject of inquiry. Responding to Agnes’s questions, Martha admits that she can no longer have children due to menopause, and that she is obsessed with smoking cigarettes. Agnes tells the doctor that “good babies” are conceived when angels whisper in a mother’s ear, while “bad babies” are born from rape. She says it is hard to tell the difference between the two kinds of babies, except that the bad ones cry, make their fathers go away, and create illnesses for their mothers. Agnes confides that her deceased mother still haunts her, but another kindly spirit, “Marie,” manifests herself through Agnes’s singing voice. Later, Mother Miriam explains Agnes’s naivete, telling Martha that the girl was denied contact with the outside world since birth and has lived in the convent since her mother’s death. Mother Miriam argues that Agnes could not have consciously killed the infant, but also maintains that no other nun in the convent is responsible. On her way back to Montreal, Martha brings ice cream to her mother, who is a patient at a nursing home. Suffering from dementia, the old woman confuses Martha for her deceased sister, Marie, who was a nun, and complains that Martha is going to hell because she had an abortion. Later, at the convent, Mother Miriam recalls that Agnes refused to eat several years earlier, and that she had bled spontaneously from a hole in her hand. Outraged that Agnes was not medically treated, Martha realizes that Mother Miriam fears modern science will tarnish Agnes’s immaculate conception of God. Sometime later, Agnes prays at the grave of Sister Marie Paul, an elderly nun who died ten months earlier. Agnes tells Martha that Marie showed her a “secret place,” at the top of a bell tower. After guiding Martha up the tower stairs, Agnes says that her mother locked her away from the world because she had a premonition of Agnes’s pregnancy. When Martha asks the girl how she became pregnant, Agnes fears the doctor’s inquiry will destroy her religious faith and runs away. Back at the convent, Mother Miriam accuses Martha of being prejudiced against Catholicism. Mother Miriam confesses that she was once married with children, who now disown her, but Martha is unmoved. The doctor contends that Mother Miriam can protect Agnes only by helping prove the girl’s legal innocence, thereby forcing an acquittal. Mother Miriam then remembers the evening Agnes conceived; Sister Marie Paul died that night, and Agnes burned her blood stained bed sheets, but reported that she was not menstruating. Sometime later, Agnes tells Martha that she deserved her mother’s emotional and sexual abuse, but Martha encourages her to think otherwise and declares her love for the girl. Back inside the convent, a nun secretly advises Martha to check the archives. There, the psychiatrist digs through personal records to learn that Agnes is Sister Miriam’s niece. When the Mother Superior catches Martha in the vault, she admits that her sister was a troubled alcoholic, but is horrified to discover that Agnes was abused. In Montreal, Martha asks her friend in the police department, Detective Larry Langevin, to look into the case, and he later uncovers information that was missing from the official report: Agnes’s chamber was the only room with a wastepaper basket. Suspecting conspiracy within the convent, Martha secures a court order to hypnotize Agnes, but Sister Miriam does not approve. As the two women argue, Martha admits that she has lost faith in Catholicism and Mother Miriam says her confidence in God was regained after hearing Agnes sing. When Martha says that Agnes’s voice reminds her of her sister, Marie, who died in a convent, Mother Superior accepts the doctor’s offer of a cigarette and the two ladies laugh, wondering if saints would have smoked. Reflecting that there are no saints or miracles in modern life, Mother Miriam consents to Agnes undergoing hypnotism, so long as she can be present. During hypnosis, Agnes visualizes the wastepaper basket and says the sisters fed her glass because they are jealous. When she sees another sister in the room and refuses to speak her name, Mother Miriam attempts to stop the treatment and Martha awakens Agnes from her trance. Martha later visits Canadian government archives and discovers that the convent has secret passageways. She explores a tunnel by candlelight and finds that it leads to a barn, where Agnes milks cows. Sometime later, Mother Miriam storms into Martha’s office and orders the doctor off the case, claiming the baby was a miracle. However, Martha convinces Justice Joseph Leveau to permit her one more day with Agnes. Back at the convent, Mother Miriam admits that she knew about the pregnancy, but swears she did not kill the baby. Martha hypnotizes Agnes again and asks about the night of conception. Agnes says that Sister Marie Paul, on her deathbed, uttered the name Michael, and Agnes interpreted her message to mean the archangel. Since Sister Marie had previously shown Agnes the secret tunnel, the girl followed the passageway to the barn, looking for the saint. The barn was filled with birds. As Agnes remembers, her palms begin to bleed, and she cries that she hates the man who corrupted her; however, when Martha demands to know the rapist’s name, Agnes replies, “God.” Agnes admits that Mother Miriam was with her during the birth, but the nun left her with the child. Agnes then strangled her baby with its umbilical cord and placed the body in the wastepaper basket that Mother Miriam had brought to the room, in anticipation of the birth. Sometime later, in court, Justice Joseph Leveau rules that Agnes is not responsible for her actions, and she can return to the convent unpunished. The girl stands and tells the court a mystical tale of a man who sang to her, spread his wings, and nestled on top of her. As she begins to repeat the man’s song, the judge orders her removal from the courtroom. Back at the convent, Agnes continues to sing from the bell tower.