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|Jane Fonda||Doctor Martha Livingston|
|Anne Bancroft||Sister Miriam Ruth|
|Meg Tilly||Sister Agnes|
|Anne Pitoniak||Dr. Livingston's Mother|
|Winston Rekert||Det. Langevin|
|Gratien Gélinas||Father Martineau|
|Guy Hoffman||Justice Joseph Leveau|
The motion picture opens in a Roman Catholic convent near Montreal, Canada. During evening prayers, the nuns hear screams coming from the room of Sister Agnes, a young novice. Agnes is found in her room bleeding profusely from an unidentified source. After Agnes is taken away, Mother Miriam Ruth discovers a dead baby in a wastepaper basket in Agnes' room.Dr. Martha Livingston, a psychiatrist, is assigned by a court two months after the birth to determine if Agnes is sane. Dr. Livingstone meets with Mother Miriam, who is highly protective of Agnes and her innocent and naive nature. Dr. Livingston interviews Agnes, who sings beautifully. Agnes does not remember the birth, and confesses to believing that "good babies" come from angels and "bad babies come from when a fallen angel squeezes in down there, and they start to grow, grow, 'til they come out down there." Agnes also says she had a vision of the Virgin Mary when she was 10 years old, and that the Virgin Mary sings through her.Mother Miriam tells Dr. Livingston that Agnes is an "innocent" who was kept at home by her mother and knows nothing about the world. She is desperate to keep Agnes innocent, and declares that Agnes could not have known what pregnancy was. Dr. Livingston visits her senile mother. The audience learns that Dr. Livingston's younger sister, Marie, was a nun and died in a convent. Martha is deeply disturbed by her visit to her mother. In a flashback, Mother Miriam tells Dr. Livingston about the time Agnes stopped eating in the belief she was getting fat, and then exhibited stigmata in her hand. Within a day, the wound healed up. Agnes takes Dr. Livingston to her favorite place, a bell tower at the convent. They argue about Agnes' mother and birth, and how much Agnes knows about sex and pregnancy.Mother Miriam tells Dr. Livingston that Agnes must have conceived on January 23, because (as the audience learns in a flashback) that is the night Agnes burned her bedsheets. Dr. Livingston looks around the convent ground, and comes to a barn full of statues of St. Michael and other angels and saints. She and a young monsignor argue about whether Martha's lack of faith will leave her unable to treat Agnes with dignity. Martha learns that Agnes' mother sexually molested Agnes, and that Agnes is Mother Miriam' niece. Dr. Livingston learns that among all the nuns, only Agnes had a wastebasket in her room. She receives permission from the court to hypnotize Agnes. Mother Miriam argues with Dr. Livingston about whether the hypnosis will strip Agnes of her innocence. Dr. Livingston reveals that she is an ex-Catholic who lost her faith, and Mother Miriam reveals her own lack of faith for much of her previous life (during which she was married and had children).Under hypnosis, Agnes admits she gave birth and that another woman knew she was pregnant, but will not reveal this person's name. Dr. Livingston discovers that a secret tunnel connects the convent's chapel with the barn on the convent property. Mother Miriam visits Dr. Livingston in her office and tries to have her removed from the case, but Dr. Livingston appeals to the police and is retained. Dr. Livingston obtains a second court order to put Agnes under hypnosis again. Mother Miriam admits that she knew Agnes was pregnant and put the wastebasket in her room, but denies she killed the baby.Under hypnosis, Agnes reveals that, the night Sister Paul died, she used the tunnel to go see "Michael" in the barn. Under questioning, she appears to describe being raped by a man. Suddenly, Agnes exhibits stigmata in her hands, and begins bleeding profusely. Agnes declares that God raped her, and that she hates God for it. She also admits that Mother Miriam was present when the baby was born, and that Agnes killed the child because it was a mistake, just like herself.In an epilogue, Agnes is found not guilty by reason of insanity. In court, she tells the judge that she heard a man singing beneath her bedroom for six nights in a row, and then on the seventh night he lay on top of her. In a voiceover, Dr. Livingston admits she does not know if Agnes' song represents a real man who came to her, or whether the singer is merely a symbol of hope to a girl who has lived a terrible life. Dr. Livingston wants to believe that Agnes was blessed by God somehow.