The movie opens on a working class street in an Irish/Italian Catholic neighborhood in the Bronx, N.Y, circa 1964
The pre-title establishing shots are of a quiet church garden with statues of saints and angels, a Russian immigrant playing a zither, a boy named Jimmy (Lloyd Clay Brown) being awakened by his mother for Sunday mass and then the title, DOUBT.
Jimmy races out of the house, passed the Russian man who asks him for a paper and coffee but Jimmy can't stop because he is late for church, and he's an altar boy on what looks like his first day serving mass.
Jimmy makes it into the sacristy at his church and dresses into his cassock, before starting to prepare the curettes of water and wine and incense, all the things he needs to serve mass. Another altar boy, Donald Miller (Joseph Foster), arrives for mass shortly thereafter. Donald is the first black student at the school. When Donald arrives, he looks at himself in the mirror and asks Jimmy if he thinks he's fat. Jimmy doesn't think so, and asks if Donald's clothes fit okay. Jimmy could care less whether anyone is fat, but Donald is body conscious and checks himself out in the mirror, unsure of himself.
Father Flynn (Phillip Seymour Hoffman) delivers his sermon as Donald and Jimmy serve mass. The church is packed, and we learn it's 1964 as Flynn talks about President Kennedy's assassination the year before and how that event was a tragedy everyone in the nation shares so, in its way, it brought people together because they all shared that event. The hopelessness and despair it created in everyone created a permanent bond between them and a spirit of "we're in this together" that should not be ignored.
Sister James (Amy Adams), a quiet young nun, sits in the pew listening intently to the sermon. She wears the archaic nun's habit: black dress, black cape, and black bonnet. As Flynn continues his sermon, he talks about a man on a cargo ship that catches fire and sinks all the while he's looking to the starts to find a constellation to guide his way home. As he talks, the camera scrolls through the church, to the very back, where more nuns sit including one who's watching all the children in church like a hawk. Spotting her prey, this nun (face unseen), rises from her pew and walks over to smack a chattering boy (Michael Roukis, as William London), in the back of the head and wake another boy who has fallen asleep. After she frightens the sleeping boy and makes him sit up straight in church, we see this nun is Sister Aloysius Bouvier (Meryl Streep).
Flynn finishes his sermon by talking about the crises of faith that sometimes enter into everyone's lives and that whenever people feel lost, they should not feel alone because even the bravest and the most faithful have doubt from time to time.
After mass, Flynn is back in the sacristy as Donald changes out of his cassock and gets ready to go home. He tells Flynn when he grows up, he wants to be a priest too. Flynn takes out a small toy - a little ballerina that dances when a mirrored magnet is applied to it. Donald is a very lonely boy who doesn't seem to have a lot of friends, and it's obvious he admires Flynn a lot and looks up to him. Flynn gives him the toy, obviously feeling sorry for Donald. (Throughout the movie, it is emphasized at every opportunity that Donald is struggling partly because he is the only black student in the Irish/Italian Catholic School).
The next day, it's Monday in the convent and all the nuns wake up and dress for the day, in their medieval habits. The students start to file into the building and London stops Sr. James and asks her what's going to be on the math test tomorrow, and if there will be a lot of long division. Sr. James starts to turn away from him, and he reaches out and grabs her arm. Sr. Aloysius sees this (it's against the rules to ever touch a nun, as they are brides of Christ and no man should ever touch them) from her perch on stairs high above the schoolyard and she shouts, "BOY! Come smartly now and don't let me wait". Flynn says to Sr. James, "The dragon is hungry". London goes up to see Sr. Aloysius, who takes unsmiling delight in disciplining the students she is clearly the Principal of the school.
Sr. James has the 8th grade class, and subjects are taught in periods. It's now history, and Sr. James is covering the New Deal and FDR, calling President Roosevelt, President Lincoln, and President Kennedy the three greatest presidents America has ever had. They're talking about FDR's "Nothing to Fear but Fear itself" speech as Sr. Aloysius enters the classroom, patrolling the rows of desk to check for any contraband, such as hair barrettes on the girls or transistor radios on the boys. She finds one boy, Conroy, with a wire running out of his ear and asks him what that is, and Conroy, a smartass, says, "I don't know, Sister. I don't know what it is." "You come with me, BOY," is Aloysius' reply, and she takes him down to her office to confiscate the radio and make him write multiplication tables over and over again.
There's a shot of choir practice for the Christmas pageant everyone is enjoying listening to the students sing, except Sr. Aloysius, who just sits there, with a rock hard stoic joyless face.
But, that coldness is just a front as we see in the next scene, where the nuns are all in their convent at dinner together. Sister Veronica sits next to Aloysius. Veronica is ancient, well in her 80's, and going blind. She can't find her fork to eat, so Aloysius slyly slides it over to her reach, never letting Veronica know she helped her. Aloysius takes care of Veronica like this through the whole movie, trying to make sure none of the priests or the monsignor figures out Veronica is going blind (because then she would be taken away from the convent and forced to live elsewhere). Aloysius is established as taking care of her convent and her school, with draconian measures when necessary.
Sr. James chews a bit of meat that's too fatty and tries to spit it out, but Aloysius makes her put it back in her mouth and eat it anyway, so as not to waste food. She does this with just a well-placed look in James' direction.
Aloysius has a bell she rings when she wants people's attention, and she rings it and asks the nuns what they thought of Flynn's sermon on Doubt yesterday. She says something must have prompted it and is suspicious of Flynn, thinking he must have done something to cause himself to have doubt, and hence that inspired his sermon. She tells all the nuns to watch him and see what they can figure out.
The next day, it's lunchtime and Aloysius talks to Sr. James about London, who faked a bloody nose so he could leave early and go smoke cigarettes on the street corner. The nuns are eating chicken chow mein, and Sr. Veronica is missing her mouth and getting food on her habit and in her sleeves. Aloysius takes water and a napkin and cleans her up, being loving and caring. She tells Sr. James not to let the children fool her and that if you pay attention, you can tell when someone is deceiving you.
Aloysius tells Sr. James that there is a chain of command to follow, leading all the way up to the Pope. If Sr. James sees anything out of the ordinary, or if the children do anything bad, she needs to tell Aloysius who will take it up the chain.
Aloysius inspects Sr. James' classroom, throwing her cough drops out (because they are just candy by another name), and telling her to watch certain female students because she wants them to graduate as virgins, so keep them away from the boys. She also lectures Sr. James because she finds a ballpoint pen on the floor, and children are not supposed to write with them because it is bad for their penmanship. She also tells Sr. James to never open the windows and to mount a framed picture of the Pope on the wall so when she writes on the board she can look into the glass and all the kids will think she has eyes in the back of her head, because she will be able to see everything they are doing.
Flynn teaches gym class and instructs the boys in basketball. He also teaches them hygiene and tells them to always have clean nails.
The priests are all shown having dinner, eating lots of red meat, laughing, telling bawdy jokes and having fun. The nuns are shown at dinner, and everything is dead silent, where they drink milk and eat with perfect posture, as Aloysius likes.
Sr. James uses the Pope glass trick to catch London sneaking over to talk to a girl in class, the one Aloysius said to keep away from the boys. Sr. James busts him, and the class is stunned, thinking she really does have eyes in the back of her head.
Flynn calls Donald down to the rectory to see him and he leaves the class.
Everyone else goes down for music/dance class, where they learn the bossa nova. Sr. James notices Flynn putting a white tee shirt into a locker during the class. Donald has not rejoined the class yet.
When they all go back upstairs to the classroom, Sr. James asks Donald if he is okay, and is clearly worried about him because something does not seem right.
That evening, Aloysius is doing chores in the garden, covering the roses for winter. Sr. James tells her that Donald seemed strange after coming back from seeing Flynn. Donald has only been at school for 2 months, and Aloysius asks if the other kids are picking on him, since he is the first black student at St. Nicholas' school. Sr. James says that Flynn protects this boy and has taken an unusual interest in him.
Aloysius: "So, it has happened. I asked you to come to me, but I hoped you never would."
Seemingly out of the blue, Aloysius assumes Flynn is molesting Donald, though words like "molesting", "sex", or "gay" are never used in the movie. It's striking, but the characters and audience know what everyone is talking about, without the subject ever being clearly defined.
As Aloysius and Sr. James talk, a handyman interrupts them so they head into the convent where the cleaning woman is bringing a cat into the kitchen to catch a mouse she saw. Aloysius tells Sr. James to tell her everything she has seen.
The film cuts to Flynn, at a table with all the boys, eating cookies and drinking lime soda, talking about girls and asking them out on dates, or asking them to dance. It looks like the 8th grade class of boys. One boy asks what happens if all the girls he asks to dance turn him down. "You become a priest," Flynn tells him.
Sr. James tells Aloysius everything she saw: Flynn called Donald down to the rectory in the middle of class and was there for a while. He looked frightened when she next saw him. Aloysius says that she should have seen this coming because as the first black student, Donald was isolated and easy prey for Flynn. She said that her job is to outshine the fox in cleverness. Sr. James says that it's all probably nothing, and Aloysius asks her why she looks like she's seen the Devil then.
Sr. James says she thinks she smelled alcohol on Donald's breath when he got back from the rectory. Aloysius says that all the priests will side with Flynn and that the nuns will have to stop him themselves. The cleaning lady walks through with the cat, holding a dead mouse in paper towels. "It takes a cat," the cleaning woman says. "Yes it does. Yes, it does," says Aloysius.
The wind has been kicking up lately, making branches fall in the garden. Wind plays a role in the film from here on out with lots of shots of leaves blowing and swirling around, symbolizing the chaos swirling around the school.
Conroy has been talking in class again. He is sent to the Principal's office, where a giant sign reading QUIET greets visitors. Flynn comes over to ask why Conroy is waiting for the Principal, but Aloysius comes out and quickly sends Conroy away she wants to talk to Flynn about Donald Miller. She tells Conroy to write multiplication tables 10 times and turn it in to her tomorrow.
To meet with Flynn, Aloysius requires elaborate rules of protocol. She can never be in a room alone with a man, and must leave the door slightly open too. Sr. James arrives to chaperone the meeting.
Aloysius has Sr. James serve tea, and Flynn wants sugar. Aloysius makes a big deal about this, as she considers it an indulgence, and she gave that up for Lent last year and forgot about it. She has to look for the sugar in a drawer, and when Flynn wants three lumps of sugar, she ridicules his sweet tooth with the same scorn she has for ballpoint pens. She also thinks Flynn's fingernails are too long. When asked if Sr. James wants sugar she says, NEVER, because Aloysius is watching her.
The ruse to get Flynn into the office to talk about Young is that Aloysius wants to talk about the Christmas pageant. Flynn wants secular songs in the pageant, like Santa Claus is coming to town or Frosty the Snowman. Aloysius thinks Frosty is a pagan song advocating magic and should be banned from the airwaves. Both Sr. James and Flynn think Aloysius is crazy. Times are changing and they need to reach out to popular things to allow the children to connect with them. Aloysius says Christmas is about Christ; so all songs should be religious.
Flynn gets an idea for a sermon on intolerance listening to Aloysius and he writes it in a little book with a ballpoint pen. Flynn tells Aloysius it is a new time and that something inside people has changed. He thinks they should sing songs from the radio, take the kids out for ice cream, and also take the boys camping. Flynn says religious people need to relate to the people in the working class neighborhood they are in. Aloysius says there's no way they can do that, because religious people are different, period.
Getting onto what she really wanted to talk about, Aloysius brings Donald Miller up, and says they must be very careful how he will be used: can't hide him, but can't put him right up front either because either way they would make him feel self conscious as the only black child in the school. Aloysius says they must be careful not to make him feel singled out because even Flynn himself singles Donald Young out for special treatment, like that private meeting the two had last week.
Aloysius plays cat and mouse with Flynn from this point out until the end of the film.
She says Donald seemed strange when he returned to class after that meeting. Flynn asks if Aloysius wanted to talk about the pageant, or about Donald Miller? He then tells Aloysius he is uncomfortable. The phone rings, but Aloysius won't answer itit just rings and rings and rings, making the room more tense. She asks Flynn what happened in the rectory, and he tells her it was a private matter. He asks Aloysius what she is accusing him of. He gets up to leave, and Aloysius says Sr. James smelled alcohol on Donald's breath. Flynn tells Aloysius to let this alone because it is not what she thinks --- Mr. McGinn (caretaker) caught Donald drinking wine in the back of the church. Flynn said he wanted to handle this quietly because if anyone else knew, he would have to make Donald leave the altar boys. Sr. James is relieved, because she says this explains everything, including why Donald was acting strangely.
Aloysius says it is easier to believe Flynn because Sr. James wants to believe him. She says, "these kinds of people are clever" and she means "child molester", but never says that word. Sr. James says Aloysius just doesn't like him because he's jovial, takes sugar in his tea, likes popular music, etc. She also says that she, too, likes Frosty the Snowman. Ask she says this, the light bulb overhead blows out, and Aloysius says, "You blew out my light". She also says that in Ancient Sparta, things were decided by who could yell the loudest and asks if that's what Sr. James is trying to do here.
Aloysius calls Donald's mother and asks her to come in for a meeting.
That next Sunday, Flynn delivers a sermon on Gossip using a metaphor of a woman on a rooftop gutting a pillow and letting the feathers fly everywhere. He says stopping gossip is like putting all the feathers back into the pillowcase impossible to do, so don't gossip. It bears false witness against neighbors, ruins reputations, and is a sin. Sr. James looks guilty. Aloysius just stares straight ahead unfazed.
The next day, in the courtyard, Sr. James and Flynn watch a crow in a tree and talk about his sermon. Sr. James asks if the sermon was directed at anyone in particular knowing it was meant for Aloysius and her. Sr. James clutches a letter from home telling her that her brother in Maryland is very sick. Flynn smokes a cigarette, enjoying another thing Aloysius does not approve of. Sr. James asks Flynn if "it is true" meaning, did Flynn molest Donald Miller. She tells him she saw Flynn put Donald's undershirt into is locker. Flynn says he just left it in the sanctuary, and that he was returning it and did not want to embarrass the boy by bringing it into the classroom, so he just put it in the locker himself.
Flynn says that Donald is a troubled boy that's why he drank the wine, and that Donald needs compassion. Flynn says he cares about the students and that everyone needs compassion.
The next day in school, one of the girls comes up to Flynn and tells him she likes a boy. He is clearly the faculty member the kids feel comfortable coming to for help and advice. Flynn sees Donald approaching, but this time he ignores and avoids him. Donald looks hurt. William London sees that Donald isn't being protected, so he slams all of Donald's books and papers onto the floor. He also breaks the ballerina toy Flynn gave Donald. Flynn sees this and immediately comes over to help Donald pick up his things. He hugs and comforts Donald. Sr. James watches suspiciously.
In history class, Sr. James tries to get Donald to tell her what was Patrick Henry's famous remark, but he does not want to talk. Another boy answers for him and Sr. James, on edge, sends him to the Principal's office for talking when he was not supposed to.
Donald's mother is meeting with Sr. Aloysius, who has been listening to the transistor radio she confiscated from a student earlier in the film. She's marveled by how small radios have gotten --- proof that her anti-tech/anti-change message doesn't always apply. She tells Mrs. Miller she likes to listen to the news all day, and has always liked the news since she became addicted while her husband was in the war, and she followed news reports all day. The husband died fighting, and so she became a nun after that, and kept up with the news after that. Mrs. Miller is surprised Sr. Aloysius was married.
Mrs. Miller says she knows Donald was caught drinking wine and is happy Flynn watches out for him so other boys don't pick on him. Mrs. Miller has been concerned about Donald graduating, and only wants her son to make it through June so he can go to a good high school where he will not be picked on.
Mrs. Miller is late for work, so Aloysius walks with her to her job. She comes out and tells Mrs. Miller that she is worried about Flynn making advances on her son. Mrs. Miller says there is no evidence of that and that maybe Aloysius is imagining it. She does not think Flynn gave her son altar wine and does not want any trouble. She keeps repeating that she just wants Donald to make it through June and graduate with no trouble.
Aloysius tells Mrs. Miller that there are men like Flynn who chase after boys, and Mrs. Miller says that maybe there are some boys that want to be caught. Without ever coming right out and saying it, she tells Aloysius she thinks Donald is gay. She tells Aloysius that Donald's father beats him because of "his nature" and not because of things he does. His father does not want a gay son, and has trouble dealing with Donald. Mrs. Miller says the reason she put Donald in private school was that the other boys were going to kill him in public school the kids don't like Donald, his own father does not like him, and Flynn was the only person ever good to Donald. She just needs Donald to make it to June and graduate. Just until June. She tells Aloysius to stop making trouble because Donald's father would kill him if Aloysius made a big deal about this if she wants to get rid of the priest, then do it, but leave her son out of it.
Walking back to church, Aloysius is caught in a big gust of wind and swept up in leaves in an approaching rainstorm just as he walks into the church to up the ante in her campaign against Flynn.
Flynn comes to talk to her to tell her to stop that campaign against him. He tells Aloysius she has nothing more than unfounded suspicions, while Aloysius accuses him of seducing Donald. He asks her why she says this, and she tells him that she's looked into his past and that she "knows people" at his previous parishes. Just then, the light bulb burns out overhead. Flynn says Donald's father beats him and that he needed compassion. Aloysius says she's had her eye on him since she saw him grab William London by the wrist once in the playground and she did not like that he touched the boy.
Flynn asks her if she's serious, and says she is imagining things. He takes out ballpoint pen and paper and says he is going to write down everything she says in case he needs it to have her removed from the parish later.
Aloysius says she called his last parish and spoke to the nuns there and they told him all about the real reason he had to leave the parish. Flynn is angry and said Aloysius broke the chain of command, because matters need to be handled by pastors, then bishops, then all the way up to the Pope, while nuns take a vow of obedience and should not break the chain of command.
Aloysius asks him again if he has seduced Donald Miller. Flynn asks her if she's ever done anything wrong, and she says yes, and then she confessed it. She also says a dog that bites is a dog that bites and needs to be dealt with so it does not bite again. She keeps asking him if he gave Donald Miller altar wine to drink. He won't answer, and she tells him that she is going to leave the office now and that if he does not confess, she will not stop pushing this until the truth comes out. Flynn stops her and says that he does not want this to get out.
Aloysius says that Flynn will ask for a transfer and take a leave of absence and that no more harm will come to Donald. Flynn says he has done nothing wrong and only cares about Donald. He says he will fight Aloysius, and she says, "You will lose". "Where is your compassion? he asks. "Nowhere you can get to it".
She tells Flynn she has no sympathy for him, and also that he needs to cut his nails.
That next Sunday, Flynn delivers his farewell sermon, stepping down from the pulpit to shake the parishioners hands and say goodbye. He says there is a wind behind everyone pushing them through life, and that now it is taking him away and that he will miss everyone. Aloysius and Sr. James are in the pews, looking stoic. Donald Miller is sad and sheds a tear. Mrs. Miller is a mix of emotions.
A few weeks later, Flynn is long gone, and Sr. James is back from visiting her brother, who has now recovered. Sr. James says that Donald's heart is broken without Flynn, and asks her if she was ever able to prove what she says Flynn did.
Aloysius says she is sure she did the right thing, while Sr. James says she can't sleep anymore because of all of this.
Aloysius reveals instead of being disciplined, Flynn was rewarded with a PROMOTION, in an F-up/Move-up scenario: he was promoted to pastor of a larger church with a larger school. The Monsignor protected him, and instead disciplined Aloysius for breaking the line of command and talking to nuns about Flynn instead of a pastor.
Aloysius admits she lied and that she never called a nun she made that up, but the lie would not have worked if Flynn had been innocent. She was sure Flynn molested boys, so she pretended she talked to a nun about him to get a reaction out of him that would prove he was guilty: and she got the reaction she expected from him.
She said his resignation from this church was his confession, but Sr. James says it is wrong to lie and that Aloysius should not have done that.
Aloysius says that in the pursuit of righting a wrong, there is a price, and that lie was the price they needed to pay to protect the boys of the parish.
Sr. James can't believe Aloysius lied.
Suddenly, Aloysius breaks down and cries. She admits that even she has doubts, "such doubts", she says.