In Los Angeles in 1928, single mother Christine Collins returns home to discover her nine-year-old son, Walter, is missing. Reverend Gustav Briegleb publicizes Christine’s plight and rails against the Los Angeles Police Department (LAPD) for its incompetence, corruption and the extrajudicial punishment meted out by its “Gun Squad” led by Chief James E. Davis. Several months after Walter’s disappearance, the LAPD tells Christine that the boy has been found alive. Believing the positive publicity will negate recent criticism of the department, the LAPD organizes a public reunion. Although “Walter” claims he is Christine’s son, she says he is not. Captain J. J. Jones, the head of the LAPD’s Juvenile Division, insists the boy is Walter and pressures Christine into taking him home “on a trial basis”.
After Christine confronts Jones with physical discrepancies between “Walter” and her son, Jones arranges for a medical doctor to visit her. He tells Christine that “Walter” is three inches shorter than before his disappearance because trauma has shrunk his spine, and that the man who took Walter had him circumcised. A newspaper prints a story that implies Christine is an unfit mother; Briegleb tells Christine it was planted by police to discredit her. Walter’s teacher and dentist each give Christine signed letters confirming “Walter” is an impostor. Christine tells her story to the press; as a result, Jones sends her to Los Angeles County Hospital’s “psychopathic ward”. She befriends inmate Carol Dexter, who tells Christine she is one of several women who were sent there for challenging police authority. Dr. Steele diagnoses Christine as delusional and forces her to take mood-regulating pills. Steele says he will release Christine if she admits she was mistaken about “Walter”; she refuses.
Detective Ybarra travels to a ranch in Wineville, Riverside County, to arrange the deportation of 15-year-old Sanford Clark to Canada. The boy’s uncle, Gordon Northcott, has fled after a chance encounter with Ybarra, who mentions his business there being a juvenile matter. Clark tells Ybarra that Northcott forced him to help kidnap and murder around twenty children, and identifies Walter as one of them. Jones tells Briegleb that Christine is in protective custody following a mental breakdown. Jones orders Clark’s deportation, but Ybarra takes Clark to the murder site and tells him to dig where the bodies are buried. Clark hesitates, but soon uncovers body parts. Briegleb secures Christine’s release by showing Steele a newspaper story about the Wineville killings that names Walter as a possible victim. Under interrogation by Ybarra, Walter’s impostor reveals his motive was to secure transport to Los Angeles to see his favorite actor, Tom Mix, and says the police told him to lie about being Christine’s son. The police capture Northcott in Vancouver, British Columbia, Canada. Meanwhile, Briegleb introduces Christine and her case to famed attorney “S.S.” Hahn who takes the case pro bono and quickly secures a court order for the release of other unjustly imprisoned women whom the police wanted to silence.
On the day of the city council’s hearing into the case, Christine, Hahn, and Briegleb arrive at Los Angeles City Hall, where they encounter thousands of protesters who are demanding answers from the city and decrying the LAPD. The hearing is intercut with scenes from Northcott’s trial. The council concludes that Jones and Davis should be removed from duty, and that extrajudicial internments by police must be stopped. Northcott’s jury finds him guilty of murder and the judge sentences him to death by hanging.
Two years later. Christine has still not given up her search for Walter. Northcott sends her a message saying he is willing to admit to killing Walter on condition that Christine meets him before his execution. She visits Northcott, but he refuses to tell her if he killed her son. Northcott is executed the next day.
In 1935, David Clay, one of the boys assumed to have been killed, is found alive in Hesperia, California. He reveals that one of the boys with whom he was imprisoned was Walter. David, Walter, and another boy escaped, but were separated. David does not know whether Walter was recaptured, but he says Walter helped him escape, giving Christine hope he is alive.
In the epilogue, it states that after the hearing, Captain Jones was suspended, Chief Davis was demoted, and Los Angeles Mayor George Cryer chose not to run for reelection. California’s state legislature made it illegal to forcibly commit people to psychiatric facilities by mere words alone of authorities, and Rev. Briegleb continued to use his radio show to expose police misconduct and political corruption. Wineville is said to have changed its name to Mira Loma to escape the stigma of the murders, and Christine Collins reportedly never stopped searching for her son.