In 1960s Pennsylvania, Mary Clancy, Hayley Mills, a rebellious teenager, is sent to St. Francis Academy, a Catholic boarding school for girls run by an order of nuns. On the train to the school, she meets Rachel Devery, June Harding, a quieter classmate. The two quickly become friends and begin challenging the school's rules and routines.
Shortly after arriving, Mary and Rachel stage pranks, including giving unauthorized tours of the cloister and tampering with food in the sisters' dining room. These acts repeatedly land them on dishwashing duty, which brings them into closer contact with the nuns. Rachel writes to her former school principal to express dissatisfaction with St. Francis Academy's discipline and curriculum. His visit prompts a philosophical discussion with Reverend Mother about educational reform, but no changes are made.
As the year progresses, Mary begins to observe the nuns more closely. She learns that Sister Ursula, often mocked for her German accent, had once protected Jewish children from Nazis during World War II. She also notices Reverend Mother performing quiet acts of kindness, including feeding birds at dawn. These moments prompt Mary to question her assumptions about the convent and its residents.
Comedic episodes continue throughout the school year. The hiring of a sophisticated dance instructor and a failed cement casting experiment add levity to the girls' experience. However, deeper emotional themes emerge. A visit to a retirement home unsettles Mary, who is confronted with the challenges of aging and mortality. Later, a smoking incident leads to a fire alarm and campus-wide panic. Reverend Mother considers expelling the girls but ultimately allows them to return after meeting Mary's emotionally distant guardian.
In their final year, Mary and Rachel join the school band and work to win a regional competition to raise funds for the school. Reverend Mother, initially hesitant, rents uniforms to support their efforts. The girls win the competition, signaling a shift in their relationship with the school.
During the Christmas break, Mary remains at the academy and quietly observes the sisters at midnight mass. A private conversation with Reverend Mother reveals her personal journey into religious life. These interactions influence Mary's growing appreciation for the nuns' spiritual commitment.
The students are later shocked by the sudden death of Sister Liguori. Rachel accuses Reverend Mother of being emotionally detached, though Mary witnesses her grieving privately in the chapel. Mary also learns that Sister Constance is leaving the school to teach at a leper colony, further reinforcing the depth of the sisters' dedication.
At graduation, Reverend Mother announces the names of students who will remain at the convent to begin their novitiate. Mary is among them. Rachel is surprised by the decision but comes to accept it. In their final exchange, Mary jokes that Rachel may return to join her. Reverend Mother dryly replies, > "If she does, I quit".
