The film opens with a series of montage shots depicting life in a white, Catholic community in the Bronx. A young boy hurriedly wakes up and prepares for his service as an altar boy during Sunday mass. As the young boy walks into the church, he pokes fun at Donald, an African-American altar boy. As the morning progresses, we are introduced to Father Flynn, the priest of the parish. He gives a powerful sermon on doubt and encourages his congregation to both admit to and embrace the feeling of uncertainty. In the congregation, we see suspicion wash across the face of Sister Aloysius, an elderly nun and the principal of the parish’s school.
Later that night, the nuns and the priests eat separate dinners. While the male clergy is rowdy and loud, the nuns eat dinner together in total silence. Breaking the tranquility, Sister Aloysius asks her colleagues about the motivations for Father Flynn’s sermon. She is under the suspicion that Father Flynn is experiencing feelings of doubt because has committed regrettable actions. She urges the other nuns to remain alert. Sister James, a young and naive nun, is clearly nervous about Sister Aloysius’s uneasiness.
The next scenes feature Donald Miller, the African-American altar boy that appeared in one of the film’s opening scenes. We learn that he is the first black student at the school, and that many of his peers bully him and treat him disrespectfully. Father Flynn appears to pay special attention to Donald—on one occasion, he gives him a toy dancer. From the contextual clues, we begin to extrapolate that Sister James and Sister Aloysius believe that Donald and Father Flynn may share an inappropriate relationship. One afternoon, after Donald returns to Sister James’s class, the young nun observes that he is acting strangely and smells of alcohol. She alerts Sister Aloysius, and the two call a meeting with Father Flynn to discuss their suspicions.
During their meeting, Father Flynn grows incredibly angry and defiant. He is frustrated that the nuns do not have any concrete evidence to prove their allegations. The priest argues that he has taken Donald under his wing because he is relentlessly bullied at school. Father Flynn insists that he caught Donald drinking the altar wine and then spoke to him privately so that Sister Aloysius wouldn’t punish him. Upon revealing this information, Sister Aloysius removes Donald from being an altar boy. Father Flynn leaves the meeting in a huff. The following Sunday, he delivers a sermon about the vicious nature of gossip.
Another day, Sister James sees Father Flynn avoid Donald in the hallway. She then watches as another student steps on Donald’s toy dancer and slaps the books out of Donald’s hands. Father Flynn rushes over to console Donald, and the audience is prompted to consider Father Flynn’s innocence and the motivations for Sister Aloysius’ accusations.
Throughout the film, it is clear that Sister James undergoes a character transformation. She becomes increasingly strict with her class, and she begins to take on the authoritative and fear-inducing leadership that Sister Aloysius encourages. Meanwhile, Sister Aloysius meets with Donald’s mother to voice her concerns. However, to Sister Aloysius’s surprise, Mrs. Miller is more concerned with her son graduating from the school than Father Flynn’s potential advances. Mrs. Miller tells Sister Aloysius that Donald’s father is abusive because he believes his son is feminine. Mrs. Miller seems to think that Father Flynn is a loving a positive male figure in her son’s life, and she chooses not to take action against the allegations.
As the fall turns to winter, Sister Aloysius is increasingly aggravated that no action has been taken against Father Flynn. As she calls the priest into her office one last time, she tells Father Flynn that she has spoken with a nun at one of his past parishes and that the nun has corroborated her suspicions. After this discussion, Father Flynn agrees to resign. He gives a final sermon to his congregation. The camera focuses on Donald Miller as he cries from the pews.
The Christmas holiday approaches, and Sister James has returned to the school after taking time off to visit her sick brother. Sister Aloysius and Sister James talk on a church bench, and the elder nun updates Sister James of everything that happened in her absence. Sister Aloysius explains that Father Flynn resigned and was given a “promotion” at another church. Sister Aloysius admits that she lied about speaking with a nun from Flynn’s former parish. However, she argues that in Father Flynn’s resignation is his admission. Sister James is aggravated at Sister Aloysius, as she believes the priest’s innocence and understands the nun’s actions to be selfish and sinful. In the film’s closing moment, Sister Aloysius cries and confesses that she “has her doubts.”