Father Flynn delivers a sermon at St. Nicholas School and Church in the Bronx in 1964. Addressing the idea of religious uncertainty, he tells a story about a cargo ship that sinks in the middle of the ocean. Everyone on board drowns except one man, who manages to build a makeshift raft. Looking up to the sky, the man navigates by the stars, using them to discern his way home. Not long after he sets his course, though, clouds appear and obscure the stars, making it impossible for him to know if he’s still headed in the right direction. For 20 nights, the sky remains starless, and he wonder if he has “seen Truth once, and now ha[s] to hold on to it without further reassurance.” Turning his attention to his listeners, Father Flynn says, “There are those of you in church today who know exactly the crisis of faith I describe. I want to say to you: Doubt can be a bond as powerful and sustaining as certainty. When you are lost, you are not alone.”
The church in which Father Flynn delivers his sermon is also a Catholic school. One day, a young nun named Sister James visits Sister Aloysius in her office. Sister Aloysius is the school principal, and she lightly scolds Sister James for being a “very innocent person.” She urges James to be more suspicious and a harsher disciplinarian. She also asks why Sister James doesn’t send more students to the principal’s office, and James says that she likes to handle classroom situations on her own.
Sister Aloysius makes it clear that she’s committed to traditional methods of teaching. She then offers Sister James advice about how to conduct herself in class, critiquing her for being too easy on the children. Sister James admits that she wants her students to feel comfortable coming to her with their problems, but Sister Aloysius dismisses this idea, saying that it’s “more important they have a fierce moral guardian” than an adult confidante. Sister Aloysius then asks what Sister James thinks of Father Flynn, wondering aloud where he got his idea for his sermon about doubt. Before Sister James leaves, Sister Aloysius leans forward and asks if she has “noticed anything,” admitting that she herself is “concerned” about “matters in St. Nicholas School.” However, Sister James doesn’t know what she’s talking about, so Aloysius simply tells the younger woman to pay close attention to her class and to report anything that seems out of sorts.
Shortly thereafter, Sister James encounters Sister Aloysius in the garden. Aloysius asksJames how Donald Muller is doing in school, and James says that he has “no friends” in class. Sister Aloysius also asks if anyone has hit Donald. When James says no, Aloysius says that someone surely will eventually. “I’m not so sure anyone will,” Sister James says, eventually adding that Father Flynn has become the boy’s “protector.” Hearing this, Sister Aloysius immediately stops what she’s doing and stands up. Sister James explains that Father Flynn has “taken an interest” in Donald ever since Donald joined the altar boys. “I thought I should tell you,” James says. “I told you to come to me, but I hoped you never would,” Aloysius replies, saying that she knew that things would be “set in motion” if James ever reported something like this to her. “So it’s happened,” she says. Sister James says, “I’m not even certain what you mean,” but Aloysius forces the younger woman to admit that she is suspicious of Father Flynn.
Sister James admits that she has been uncomfortable ever since Sister Aloysius instructed her to be more diligent and skeptical. “I want my peace of mind,” she says, suggesting that she feels “less close [to] God” now that she’s been trained to think so cynically. Nevertheless, Aloysius tells her that she can’t have “peace of mind,” since it’s her job to protect the children. Aloysius then urges James to tell her more about what happened, and James admits that Donald Muller had alcohol on his breath after spending time alone with Father Flynn. Hearing this, Sister Aloysius decides that she and Sister James need to do something. However, she explains that she can’t simply take the news to Monsignor Benedict, who has the most power at the school. She knows Monsignor Benedict would simply ask Father Flynn about the incident and then naively believe anything he might say in his defense. As a result, Aloysius tells James that they will have to go directly to Father Flynn—an idea Sister James hates, since she herself hasn’t fully decided to pursue the matter. Nonetheless, Sister Aloysius hatches a plan to call Father Flynn to her office on the pretense of discussing something else. Then she will bring up the situation regarding Donald Muller.
Father Flynn comes to Sister Aloysius’s office before Sister James arrives. The nuns aren’t allowed to be alone with men, so he waits outside until Sister James appears, at which point they both enter and begin a discussion about the Christmas pageant. Father Flyn suggests that the children sing a secular song in addition to the traditional hymns. Sister James likes this idea, proposing that they sing “Frosty the Snowman.” Flynn agrees, but Sister Aloysius interrupts, saying that the song “espouses a pagan belief in magic” and is “heretical.” Father Flynn takes out a notebook to write down an idea for a sermon, explaining that he has to jot down his ideas so he doesn’t forget them. When Sister Aloysius asks what he’s writing, he says, “Intolerance.”
Sister Aloysius then says that they will all have to be careful about how “Donald Muller is used in the pageant,” since he is the school’s only black student. When Father Flynn says that he thinks Donald should be “treated like every other boy,” Sister Aloysius points out that he himself has “singled” Donald out for “special attention.” She then brings up the fact that Flynn had a “private meeting” with Donald in the rectory. Suddenly, Father Flynn senses that “something’s up,” so he asks what, exactly, Sister Aloysius is getting at. At this point, Aloysius reveals that Donald acted “strangely” after his meeting with Flynn. Before long, Flynn understands that Aloysius is suggesting that he has had inappropriate relations with Donald. Taking issue with Aloysius’s “tone,” he says that he’s “not answerable” to her. He then claims that he caught Donald drinking altar wine. Because Donald is the only black student at the school, he upholds, he decided not to tell anyone what happened. Now, though, he’s going to have to remove Donald from the altar boys, since news has gotten out about his drinking.
When Father Flynn leaves, Sister James is relieved. She wholeheartedly believes that he has told the truth, but Sister Aloysius isn’t so sure, thinking that believing him would be the “easy” way out of the situation. This bothers Sister James, but Sister Aloysius simply picks up the phone and calls Donald Muller’s mother, asking her to come to the school at her earliest convenience.
Shortly after his conversation with Sister Aloysius, Father Flynn delivers a sermon about the dangers of gossip. Around this time, he encounters Sister James in the garden and insists that he’s innocent, claiming that Sister Aloysius is ruining his reputation simply because he has a softer and more contemporary approach to teaching. He insists that he has only tried to be supportive and compassionate, and this message resonates with Sister James, who says that she believes in his innocence.
Meanwhile, Sister Aloysius speaks with Mrs. Muller in her office. Mrs. Muller is worried that Donald is in trouble, since she’s especially concerned that he does well in school. She explains that he simply needs to make it through June so that he can graduate the eighth grade and get into a good high school. When Sister Aloysius tells Mrs. Muller the real reason she wanted to talk to her, Mrs. Muller is hesitant to pursue the conversation. Thinking that Donald will get in trouble because of what Father Flynn has done, she makes it clear that she doesn’t want to do anything about the situation. She then hints that Donald might be gay, but Sister Aloysius disregards this, wanting to focus only on Father Flynn’s actions. When it becomes clear that Mrs. Muller won’t do anything to stop the situation, though, Sister Aloysius says she will kick Donald out of school if that’s what it takes to protect him. Mrs. Muller simply gets up and leaves, saying that she only wants what’s best for Donald’s future.
After Mrs. Muller leaves Sister Aloysius’s office, Father Flynn enters in a rage. He tells Aloysius that she has no right to address this matter on her own. “You answer to us!” he yells. Still, she tells him that she called his former parish and spoke to a nun who told her that he abused a child there as well. This is a lie, but he doesn’t know this, and his explosive reaction convinces Sister Aloysius that her suspicions have been correct all along. She also tells him that she will continue to call his former parishes until she finds parents who are willing to speak out against him. She then leaves him alone in the office, at which point he picks up the phone and calls the bishop.
Not long after her final confrontation with Father Flynn, Sister Aloysius sits in the garden with Sister James, who admits that she hasn’t been able to sleep since she started thinking about Flynn’s relationship with Donald. “Maybe we’re not supposed to sleep so well,” Aloysius says, adding, “They’ve made Father Flynn the pastor of St. Jerome. […] It’s a promotion.” Going on, she says that she went to Monsignor Benedict after her final conversation with Flynn. “He did not believe it to be true,” she says. She also tells James that she lied to Flynn in order to discern the truth, and when James expresses her surprise that she would sin in this way, Aloysius says, “In the pursuit of wrongdoing, one steps away from God. Of course there’s a price.” Then, after thinking for a moment about the fact that Flynn has become a pastor, she says, “I have doubts! I have such doubts!”
