In 1964 Mississippi, three young civil rights activists – one of whom is African American – drive through Jessup County at night. Three cars pursue and run them off the road. Approaching the boys’ car, the pursuers shine flashlights in their faces. One of the men, a police officer, accuses the driver of speeding and uses racial epithets to refer to him and his companions. Another man sniffs the driver and says he smells like an African American, then shoots him in the head. All three are killed, and the men laugh and congratulate themselves afterward. The boys are reported missing, and Federal Bureau of Investigation (FBI) agents Alan Ward and Rupert Anderson are assigned to the case. They get to know each other on the drive to Jessup County, and Anderson, a native of Mississippi, irritates Ward with his joking comments about the Ku Klux Klan (KKK), a secret white supremacist organization. Although Anderson insists on calling him “Boss,” Ward says he was only put in charge because he worked on a civil rights case in Oxford, Missisippi. At the Jessup County police station, the agents meet Deputy Clinton Pell, who jokes that FBI stands for “Federal Bureau of Integration.” Sheriff Ray Stuckey introduces himself, and they discuss the three missing boys, who were arrested for speeding by Deputy Pell and held from 3 p.m. to 10 p.m. on June 21st. As he and Anderson leave, Ward wonders why the boys did not make a phone call from jail, as they were activists who had been trained to follow such protocol. Anderson defends Sheriff Stuckey, saying he used to be a sheriff, himself, and never lied. At a busy diner, Ward takes a free seat in the “colored” section while white patrons stare him down. He attempts to speak with Hollis, a young African American man, about the missing boys, but Hollis leaves the table. Later, discussing the case with Anderson, Ward recalls that the missing boys originally came to Jessup to set up a voter registration clinic at a church. However, the KKK stopped them by burning the church down. The night they went missing, the boys were returning to apologize to the congregation. Despite Anderson’s insistence that African American locals will refuse to talk to them, he accompanies Ward to the home of an older man who was burned in the church fire. His wife explains that he was attacked by four white men outside the burning building, and although she told the three civil rights activists about the attack, she refuses to identify the men again. That night, Hollis, the young man at the diner, is severely beaten by three white men who warn him not to talk to the FBI. As they study pictures of the missing boys at their motel, Anderson tells Ward a story about his father, who sabotaged a prosperous African American farmer by poisoning his mule and eventually ran him out of the state. He says that, like other bigots, his father’s need to feel better than African Americans stemmed from his own poverty. A rock crashes through their motel window and the agents discover a burning cross outside. Although Anderson discourages him, Ward requests more FBI agents from Washington, D.C. headquarters, and sets up an office at a defunct theater in the middle of town. Ward and Anderson discover that Clayton Townley, a local businessman, is the “Grand Wizard” of the local KKK. Meanwhile, FBI Agent Bird gets word that the boys’ car has been found on a Native American reservation. There, as the car is towed out of a swamp, Ward tells Bird they need 100 more men to search the swamp for bodies. Again, Anderson discourages Ward, insisting he will “start a war” by bringing in more people. At night, masked KKK members set fire to African American churches, schools and homes in Jessup, attacking the people inside. The following day, at the site of one of the burned-down churches, a young boy named Aaron Williams addresses fellow parishioners with a hopeful speech about race equality. People scatter as Ward and Anderson approach, but Aaron and his father, Vertis, remain behind. Although they do not reveal much, Aaron suggests the FBI agents take a closer look at local police. Ward and Anderson visit Deputy Pell’s home that night. As Ward goes over Pell’s whereabouts on June 21st, Anderson follows his wife, Mrs. Pell, into the kitchen and flirts with her. Leaving the house, Ward tells Anderson that Pell’s alibi includes a fifteen-minute period that only Mrs. Pell can confirm. Anderson says he noticed a wedding picture inside the house in which Pell’s groomsmen are flashing a KKK symbol. Later, Anderson brings flowers to Mrs. Pell at home and asks about the fifteen-minute window that Deputy Pell claims he spent with her on June 21st. Mrs. Pell attests to it. Elsewhere, the KKK attacks an African American congregation as they leave church. One of the Klansmen kicks Aaron as he prays and warns him to stop talking to the FBI. Although Jessup is a dry county, Anderson locates a secret bar frequented by Deputy Pell and his friends. There, a man named Frank Bailey warns Anderson that the boys will never be found. Anderson responds by grabbing Bailey’s groin until he falls to the floor, then asks Pell if he ever shoots people. After hearing reports of the incident, Ward reprimands Anderson for his unprofessional tactics. Staking out the police station, they watch as Pell releases a young African American man from custody and a truck full of KKK members drives up to kidnap him. Ward and Anderson wait to pursue the truck until Stuckey and Pell have gone back inside. Although a crossing train holds the agents back, they eventually find the African American boy wounded in a forest. The next day, Ward identifies Stuckey and Pell’s pattern, saying that on June 21st, they held the civil rights activists at the police station until KKK members could be organized for an attack. Anderson believes Pell was present for the murders, and they question him again, but the deputy remains steadfast, denying his affiliation with the Klan. When another house is burned down, Aaron helps Ward and Anderson identify the attackers. The men are tried and found guilty, but the judge claims their crimes were provoked and suspends their sentences. In retaliation, the KKK sets fire to Aaron’s family farm and lynches his father. As Clayton Townley leads a KKK gathering under the guise of a “political rally,” Anderson finds Mrs. Pell at the beauty parlor where she works. Crying over the hatred she was taught as a child, Mrs. Pell confesses that her husband took part in the missing boys’ murders and identifies the spot where their bodies are buried. Anderson embraces her and they kiss. The next afternoon, the bodies are found. At Stuckey’s urging, Deputy Pell returns home to beat his wife, as Frank and two other Klansmen look on. After seeing Mrs. Pell in the hospital, Ward agrees to help go after Deputy Pell. An FBI specialist is called in to pose as an African American local. Wearing a Klan mask, he kidnaps Mayor Tilman, who is close friends with Stuckey, and threatens to castrate him. The mayor names Pell and Frank Bailey as the boys’ murderers, and says five others were involved in the crime, including Stuckey, who was not present but helped. Because a local judge will never convict them, Anderson and Ward aim to indict the men on civil rights violations so they will be tried by a Federal court. Later, they manipulate another confession from Lester Cowens, a Klansman who admits to shooting the African American activist in the buttocks but denies killing him. Later, Anderson and Ward find Pell at a barbershop, where Ward allows them privacy so that Anderson can beat the deputy. That night, Cowens is kidnapped and hanged by men in KKK masks, but FBI agents intervene and save him. Although his attackers were secretly FBI agents, Cowens believes the KKK has turned on him and provides a full confession. Deputy Pell, Frank Bailey, and Clayton Townley are arrested and sentenced to ten years in prison for violation of civil rights laws. Lester Cowens is sentenced to three years, and the other men at the scene of the crime, Floyd Swilley and Wesley Cooke, are sentenced to seven years. Sheriff Stuckey is acquitted, and Mayor Tilman commits suicide. Anderson visits Mrs. Pell at her home, which has been destroyed. He asks what she plans to do, and she says she will stay in Jessup, claiming that enough people believe she did the right thing. Before they leave town, Ward and Anderson attend a funeral for the African American activist, whose headstone has already been desecrated.