In 1964, three civil rights workers – two of them are Jewish and one of them is black – go missing while they are in Jessup County, Mississippi, organizing a voter registry for African Americans. The FBI sends Alan Ward and Rupert Anderson to investigate. Ward is a Northerner, senior in rank but much younger than Anderson, and approaches the investigation by the book. In contrast, Anderson, a former Mississippi sheriff, is more nuanced in his approach. The pair find it difficult to conduct interviews with the local townspeople, as Sheriff Ray Stuckey and his deputies influence the public and are linked to a branch of the Ku Klux Klan.
With the help of the son of a local pastor, the FBI is finally able to bring forward a witness who saw Klansmen fire bomb a house, and three white men are arrested and tried for felony arson. A local judge, however, gives the men a token suspended sentence while deriding the FBI as "outside agitators" who provoked the white men to violence. He then releases the men who promptly attempt to kill the witness and hang his father. The FBI evacuate the family to the north and realize they will receive no help at all from local authorities.
Meanwhile, Anderson has developed a close relationship with the wife of Deputy Sheriff Clinton Pell who, in a tearful confession, reveals to Anderson that the three missing men have been murdered by her husband and his Klansmen accomplices who then buried the bodies in an earthen dam. After the bodies are discovered, revealing to the nation that the disappearance of the civil rights workers was in fact murder, Pell beats his wife brutally in retribution after discovering her betrayal.
Ward and Anderson's different approaches spill over into a physical fight which Ward wins but he concedes that his methods have been ineffective and he gives Anderson carte blanche authorization to deal with the problem in his own way. Anderson devises a plan to indict members of the Klan for civil rights violations, instead of murder, because civil rights violations are federal crimes which means that convictions for civil rights violations are more certain compared to state-level charges of murder. The FBI arranges the kidnapping of Mayor Tilman, taking him to a remote shack, where he is left with a black man, who threatens to castrate him unless he speaks out. Tilman gives him a complete description of the killings, including the names of those who were involved in it. The abductor is revealed to be an FBI operative who has been assigned to intimidate Tilman. Although the obtained information is inadmissible in court because it was obtained by coercion, it still proves to be valuable to the investigators.
Anderson and Ward concoct a plan, luring identified Klan collaborators to a bogus meeting, but the men soon realize that they have been set up and they leave the bogus meeting without discussing the murders. The FBI then concentrates on Lester Cowens, a Klansman of interest who exhibits a nervous demeanor, which the agents believe might yield a confession. The Feds pick him up and interrogate him. Anderson stages a tussle with Pell at the local barbershop in retaliation for the attack on his wife and takes off. Later, Cowens is at home when a shotgun blast shatters his windows. After seeing a burning cross on his lawn, he attempts to flee in his truck but is caught by several hooded men who intend to hang him. The team arrives to rescue him, having staged the entire scene where the hooded men are revealed to be other FBI agents.
Cowens, believing that his redneck brothers have threatened his life because of his admissions to the FBI, finally incriminates his accomplices. The Klansmen are all charged with civil rights violations, because this crime can be prosecuted at the federal level (murder was a state-based charge in 1964). Most of the perpetrators are convicted, while Stuckey is acquitted of all charges. The FBI later finds Tilman has hanged himself, and Bird wonders why. Ward tells him Tilman was guilty -- for being a witness. Mrs. Pell returns to her home, which has been completely ransacked by vandals. She resolves to stay and rebuild her life, free of her husband. Before they leave town, Anderson and Ward visit an integrated congregation, gathered at an African-American cemetery, where the black civil rights activist's desecrated gravestone reads, "Not Forgotten."
