On March 9, 1928, Christine Collins (Angelina Jolie) wakes her son Walter (Gattlin Griffith). After measuring his height against the wall gets him ready for the school day (joking around with him the whole way). She drops him off at school and goes to her job as a supervising phone operator at a Los Angeles telephone company. At the end of the day she picks Walter up at school on a cable car and he tells her that he got in a fight when another student said that Walter's father hated him. Christine corrects him by saying his father didn't even know him, so how could he hate him. Christine then explains that Walter's father was merely frightened of the responsibility that came with Walter and took off before he would have to deal with it, and Walter smiles and accepts this explanation. The next day Christine gets a phone call early saying that she has to come in since one of the other girls was sick. Eventually she agrees, disappointing Walter with the news that they have to go to the movies tomorrow, to which he sighs but nods. She tells him that there's a sandwich for him in the fridge and reminds him that a couple neighborhood girls will be by later to check on him, and she then heads out.
At the phone company, Christine is getting ready to leave when her boss Ben Harris (Frank Wood) stops her. He notes that she's done a great job as a supervisor and says that there may be an opening for a full-time assistant manager. She thanks him for the opportunity and they agree to discuss it over dinner the next night (although he obviously wants it to be more date and less business). Floating on cloud nine, Christine goes home and finds Walter missing. She searches the whole neighborhood and asks other children, but no one has seen him. Finally she calls the police, but is told by the man who answers, Detective Lester Ybarra (Michael Kelly) that most missing children turn up by morning and she shouldn't worry, he's probably just somewhere in the neighborhood and lost track of time, and that she's saying nothing that other mother's who've called haven't said. He offers to take her address, but she hangs up. The next morning, a police car comes and two cops take down her information and info on what Walter looks like, including taking a picture of him.
During the next few weeks, we see the investigation in various stages, led by captain J.J. Jones (Jeffrey Donovan), the head of the missing persons department. While they are conducting their investigation, Christine is doing her own investigation, calling various cities as far away as Las Vegas on a regular basis and seeing if any children fitting Walter's description have been found. At the same time, we see radio preacher Rev. Gustav Briegleb (John Malkovich) praying for Christine and for the safe return of Walter with his congregation (despite the fact that neither she nor Walter are members of his parish) while at the same time lambasting the corrupt and lazy police force. After five months of this, though, they are no closer to finding Walter than when they started. Meanwhile, in a town in Illinois called Dekalb, we see a man and his son (Devon Conti) at a hole-in-the-wall diner. The man reaches for his wallet to pay but realizes he forgot it at home. The owner gets pissed but decides to give the man twenty minutes to get to his house, pick up his wallet, and return to pay (with his son left as collateral). After two hours of waiting, though, the owner, now both angry and worried for the kid, decides to call the cops.
Back in Los Angeles, we see Christine moving listlessly through her job when Jones and Lester show up with some good news for her -- they have found Walter. After a big celebration at the company, Jones and Lester, along with Chief of Police James E. Davis (Colm Feore) escort Christine to the train station where in the midst of a big media circus she is reunited with....the boy from the diner. She states that that is not her son, and Jones explains how five months in captivity can both change how a person is remembered and how he or she looks in real life. Jones then asks the boy who he is and his address, and the boy gives the correct answers, but in a tone of voice that makes them sound like lines memorized for a play. Despite this, Christine eventually states that Jones may be right and after posing for a photo with "Walter" for the newspapers takes him back home.
That night, Christine and the boy are having dinner and she begins noticing things. First, the boy doesn't use manners, something Walter had been studious about. Second, and even more glaring, she notices as she is toweling him off after a bath that he is circumcised. Her eyes narrow and she drags the boy to where she had measured Walter back in March, only to find that this child is three inches shorter than Walter at the same time. This prompts her to visit Jones, who assures her again that they found the right boy -- almost demanding it, actually -- but he agrees to send a doctor over to verify.
The next day, Dr. Earl W. Tarr (Peter Gerety) arrives for the examination, but he barely does more than check for a sore throat before giving Christine the same spiel Jones gave her, only now including such tidbits as the fact that the spine can shrink in stressful times and that the kidnappers may have circumcised the boy themselves. She still refuses to believe this, though. That night, the boy is going to bed in Walter's room when he makes the mistake of saying "Good night, mommy", which causes Christine to fly into a rage, flinging a plate against the wall near his head and screaming that she wants her son back. Later, after the boy is asleep, she goes into Walter's room and apologizes to the boy for yelling but again asserts that they are not related. The next morning, Christine is woken by a phone call from none other than Gustav, who tells her to read the front page of the times and then stop by his church for breakfast. Sure enough, the days article is about her denying that the boy is her son despite the best efforts of the valiant officers and indisputable evidence that the boy is her son and how the police fear for the child's blah-blah-blah. Gustav then tells Christine the story of how Davis became chief and his first action was to give the biggest, toughest cops machine guns and then let them kill all the criminals they could -- not to eliminate crime, but to eliminate the competition. He then warns her of what she may be getting herself into, but notes that if she pulls this off, she could be the last woman to have the wrong child returned.
We then see Christine at Walter's dentist, who notes that Walter had a piece of muscle preventing the gap between his teeth from closing, which this boy does not have -- his teeth are even, something which he is eager to put in writing for her. The case is the same with school, where Walter's teacher is not remembered by the boy despite her teaching Walter for over a year and when "Walter" is unable to find his assigned desk, giving the teacher ample cause of her own to put her belief that this is not Walter Collins in writing, along with a promise to testify in court. Soon, we see Christine on the steps of a courthouse telling reporters that the police were wrong and she has proof of it. Naturally, this angers Chief Davis to no end and he orders Jones to take care of it. Jones has Christine and the boy brought in and after a heated "conference" wherein he calls her either delusional or a liar (or a pathological liar), he asks her one more time if that boy is her son. When she says no, he nods to two people and they take her away to an insane asylum where after being subjected to a very crude and harsh entrance examination series she is to be held for her own safety and the safety of the boy until such time as she can demonstrate that she is sane and capable of taking care of herself and the child.
Meanwhile, in Wineville (modern-day Mira Loma), near Riverside, we see Lester investigating a missing child report regarding a kid from Canada. He pulls over at one point to ask a stranded motorist for directions to the Northcott Ranch. The motorist, who just happens to be Gordon Northcott (Jason Butler Harner), the owner, pales a little and happily gives him the directions. Lester thanks Northcott and heads on his way to the seemingly deserted homestead. After poking around some he finds his quarry, one Sanford Clark (Eddie Alderson), and informs him that he's going back home to Canada as at the same time we see Northcott in a train station, trying to buy a one way train ticket to Canada, although the best he can do is get a ticket to Seattle where he would then have to either hitch, rent a car, or walk across the border.
Back with Christine (who has missed her appointment to appear on Gustav's show, much to his disappointment), we see her having her first breakfast in the asylum. She meets a woman named Carol (Amy Ryan) who is both sane and aware of her situation. Like Christine, Carol and a number of other women there were all brought in under a "Code 12" designation, which, while loosely defined, essentially means that they pissed off a police officer in some way, with Carol's reason being that she was someone who "worked" nights (to which Christine blushes) when a customer got a little rough, but when she filed a complaint, she found out that the customer was a cop. The available options, according to Carol, are to either keep your mouth shut and go home; behave by the asylum's rules and stay in one piece, but on the inside; or fight the system and end up with repetitive shock treatments. After breakfast, Christine has her first appointment with the head doctor, Dr. Johnathan Steele (Denis O'Hare). Christine tries to behave like she needs to to get out, but his dismissive treatment of her and accusations of lying/craziness, coupled with the photographic evidence of her posing with the boy in a front page article about mother and son being reunited, eventually cause her to start stuttering and trying to explain which only ends up making her look more insane, much to her dismay.
Meanwhile, we see Sanford in a waiting room somewhere with other kids, one of whom keeps banging a ruler up and down, causing Sanford to see a man with an axe hitting something and covering himself with blood every time the ruler comes down. After a while, he is brought in to see Lester and Lester asks why Sanford wanted to see him again. Sanford then tells Lester the story of how he had intended to only stay with his cousin at his ranch for a little while, but was eventually forced to stay there. Lester lights a cigarette and starts asking what that has to do with it, and Sanford tells them of something they would do. Every now and then, they would go driving in the city and pick up a boy who was alone by saying that his parents were in the hospital and they needed him to come with them now. According to Sanford, if just an adult asked, the kid would automatically refuse to get in, since they wouldn't take a ride from strangers. However, if they saw that there was already a kid in the car -- a kid like Sanford, for instance -- then it must be okay to get in. After they had the boy, they would take him back to the ranch and lock him up inside the chicken coop on the grounds, sometimes with as many as four or five others. Once things started to get crowded, Northcott would take some of the boys and hack them to death with an axe....except sometimes, he wouldn't go all the way, and he would force Sanford to finish. In either case, Sanford would then have to dig a grave and bury the bodies on the grounds.
By the end of this story, Sanford is in tears and Lester is in shock, with his cigarette having burnt all the way down without having been smoked. Pulling himself together, Lester asks if Sanford would remember the faces of those boys and Sanford nods yes. Lester pulls out a stack of pictures of missing boys and Sanford starts going through them. He puts the ones he recognizes face up on the table in front of him, eventually creating a pile of ten or fifteen pictures, with only a few rejects. Lester starts going through the recognized pile, looking at the names on the back. He pulls out one and asks Sanford if he's sure, and Sanford nods. Lester whispers, "Jesus Christ," and puts the picture, which is labeled "Walter Collins -- Age 9" on the table. He heads out of the room, grabs two other cops, and after grabbing Sanford and telling the cops he'll explain on the way, heads out.
The next day, Christine is having another "talk" with Steele and, after noting that she is having to be force fed her medication, informs her that if she is willing to sign a contract saying that she was wrong and the police found the right boy, then she could go home first thing tomorrow morning. She refuses and grows angry, causing the doctor to yell for an orderly, who drags Christine out of the room kicking and screaming. Carol, who is near all this, comes to Chrstine's defense by fighting with several of the nurses and orderlies and even going so far as to punch the good doctor. Naturally, this unruly conduct gets her some time in the shock treatment room. When Christine checks on her later, Carol admits that she's been pregnant twice and lost the baby twice. She tells Christine that the important thing is to keep fighting, and as for the doctors and orderlies...."Fuck them and the horse they rode in on." Christine laughs at this unladylike remark and Carol says that there's a place and time for being ladylike, and this is neither.
Meanwhile, Lester and his crew (including Sanford) reach the ranch and after securing the site they grab a shovel and tell Sanford to show them where the bodies are buried. He takes them to a spot that may once have had a small coop but now holds just the base of it, the rest having perished in a fire. Lester tells Sanford to start digging, which he reluctantly does, eventually unearthing first a shoe with a skeletal foot, then a hand, then a pair of ribcages. As Lester's partners recoil in shock and/or disgust, Lester steps forward and tells Sanford to stop, which, after a brief struggle, he does, collapsing in the dirt and crying.
Later, Jones is talking with Lester on the phone about Lester's discovery and the implications, especially those in the Collins case, when Gustav shows up with an army of lawyers demanding Christine. Jones quickly tells Lester to just get Sanford to the station and confronts Gustav. Fortunately (except for Jones), Gustav is able to get Christine's current location. The day after, we see Christine at roll call (where the inmates stand outside their doors to be counted). Steele asks Christine if she's ready to sign the contract and she says proudly, "Fuck you and the horse you rode in on." Steele orders immediate shock treatment and heads for his office just as Gustav is barging in with his army. As Gustav yells at the head nurse to bring Christine out, an order is given to nurses in the shock room to let Christine go and bring her to Steele's office. He tells her that she can leave, which she does without knowing quite why. As she departs, we see the headline on the paper he is holding -- "Bodies of missing children found at ranch -- Collins child believed dead" (not exactly it, but close enough). Christine walks outside and overhears a newsie shouting the headline and faints, but Gustav is suddenly there to catch her and take her home.
Sometime later, we see the fake Walter being interviewed by Lester. He claims innocence, but Lester says that given the Collins boy's death, he could be charged with accessory to murder. The kid doesn't believe it, but when Lester mentions that Sanford is going to jail at only fifteen (probably not true), he starts talking. Meanwhile, in Vancouver, we see Northcott arriving home at his sister's house. She welcomes him and after saying hello she invites him to go upstairs and clean up. As soon as he does, though, they hoof it and call the mounties, who are soon arriving to arrest Northcott.
Back in the states, Christine receives a visit from Gustav. He has brought a friend with him who he introduces as S.S. Hahn (Geoffrey Pierson). Gustav asks Caroline what her next step is and she brings up the idea of a civil case against the whole department. In turn, Gustav notes that he tracked down the only lawyer to go up against the city four times in civil cases and wins, but that he was much costlier than Gustav could afford. Christine nods sadly, at which point Hahn says that that's why he's doing this case pro bono. On top of that news and the subpoenas being filed against the department, including Jones and the chief, Christine and her new friends also manage to get all the women in the asylum that were placed there under Code 12 released -- including Carol, who shares a warm smile with Christine as she makes her way out.
About two weeks after this all started, on October 4, 1928, we see Christine and company heading into the courthouse amidst a swarm of people all carrying signs insulting the integrity of the LAPD. Inside the court, we see representatives of all parties gathered except for the LAPD. A recess is called, to the committee heads displeasure, and Christine is taken to a separate courtroom where the trial of Northcott is being held and where he enters a plea of "Not guilty". In the audience, a woman taps Christine on the shoulder and identifies herself as Leanne Clay (Lily Knight), a mother of one of the boys Northcott killed, which gives the two women an instant connection. On the same day, we see the fake Walter -- really a boy named Arthur Hutchins -- being reunited with his real mother by a smiling Chief Davis, who wants the press to note that the LAPD does many good deeds despite the bad deeds undertaken by a minority of the department. Unfortunately for him, this line gets derailed once the boy pipes up that it was the police who told him to be Walter Collins, which has Davis all but shoving the boy onto the train just to get rid of him. At this point, clips from each trial are shown, with people such as the Chief, Walter's teacher, and Walter's dentist testifying.
Most prominently shown is a clip of Captain Jones being interviewed wherein Hahn gets him to admit that he sent Christine to the mental hospital without warrant or cause. Eventually, the trials are concluded and verdicts are reached. For Northcott's case, it ends with him being found guilty, at which point he pauses to say that he hates everyone in the courtroom except for Christine, who he calls a real classy lady. He is sentenced to solitary confinement at San Quentin prison until October 2, 1930, at which point he will be hung from the neck until dead. In the civil trial, the decree is that Jones shall be permanently suspended (re: fired); Davis shall be demoted from his position as chief; and an internal review of the steps needed to allow someone to be committed shall be undertaken so that events such as those which allowed Christine and the other women to be committed so easily shall not happen again.
Two years later, on September 30, 1930, we see Christine at work. She takes her ten-minute "break", which consists of calls to missing child departments, when she is interrupted by none other than Hahn, her old lawyer friend. He informs her that Northcott has requested that he see her so he can tell her face to face what really happened to Walter. She goes down the next day but once the two are together, Northcott clams up. He says that he has confessed to God and been forgiven by Him and claims again that he never killed Walter, who he had called an angel at the trial, and that he does not want to lie now, lest he go to Hell. Christine demands to know what happened and that he tell the truth, even going so far as to throw him against the window to get him to talk, but it has no effect. She stays for the hanging the next day.
Northcott is calm and detached, making conversation with the reverend and saying he has no final statement. He loses control on the steps to the noose, though, and is carried up by two guards. A bag is placed over his head and the noose is fitted as straps are tightened around his body to ensure a minimum of struggling, lest the rope break and the whole thing be ruined. As the time approaches, Northcott strangely begins to sing "Silent Night". At the appointed time, the warden nods and the floor drops. Northcott jerks briefly, but after a minute is still.
Years pass. We next see Christine on February 27, 1935. Her operator friends are holding an Oscar party at one of their houses, but Christine declines, saying that she has too much work. Ben pops his head in her office and also asks, but she declines.... although after a moment, she tells him that if "It Happened One Night" (her pick for best picture) wins best picture over his pick, "Cleopatra", then she'll have dinner with him tomorrow night. Sure enough, that is just what happens. As she grins in her office, the phone rings. She picks up expecting it to be Ben, but is instead surprised by Leanne Clay, who says that they found one of the missing boys.
Christine runs to the Lincoln Heights precinct and meets with Leanne and her husband, who are watching in a viewing room as Leanne's son David (Asher Axe) is interviewed by Lester. David says that he was in there with four other boys -- two brothers named Winslow, a kid named Joseph...and Walter. One night, three of the boys staged an escape thanks to some loose fence on the coop. Joseph and Walter got out quickly, but David got stuck on the fence. As Walter runs back to get him loose, lights are turned on in the house and Northcott and Sanford realize that the kids are missing. Walter frees David and the two run for it as Northcott tried to give chase. They all went in separate directions, and David never saw either of the other boys again.
Eventually he found a house where a woman took him in, and that's where he had been staying until coming forward. Lester asks why he waited, and David says that he was scared that he'd be blamed for some of the deaths or that he'd be in some kind of trouble, at which point his parents come in and engulf him in a huge family hug, which Lester almost breaks up before deciding to let them have their moment. He and Christine head outside and he consoles Christine, saying that what Walter did was incredibly brave. She agrees and he asks what she'll do now. She smiles at him and says that if David escaped and survived, then maybe that means that Walter and the other boys also did, and that maybe Walter is out there right now, alive but afraid to come forward, thinking that something might happen to him or to his mother. Whatever the case, she says, she now has something she didn't have before. Lester asks her what that is, and she looks him in the eye and says simply, "Hope."