-In 1964, after 3 civil rights workers are reported missing, 2 FBI agents are sent to investigate in rural Jessup County, Mississippi, which is modeled after Neshoba County, where the real murders took place. The 2 agents go different ways about investigating this; Agent Alan Ward(Willem Dafoe), a young liberal northerner, takes a direct approach to the investigation while Agent Rupert Anderson(Gene Hackman), a former Mississippi sheriff who understands the race relations, takes a more gentle approach
-It's hard for the 2 to work in town, as the local sheriff's office is linked to a major branch of the KKK, and the agents can't talk to the local black community due to their fear of KKK retaliation. Slowly but steadily, relations between the FBI and local Jessup County sheriff's office break down. Things boil over when the bodies are found and the sheriff deputy, Clinton Pell, realizes his wife gave their locations to Anderson, and he assaults her. When Anderson sees her in the hospital, he rushes off to confront Pell, but is stopped by Ward. After a brief fight, the 2 agree to work together and bring down the Jessup County branch of the KKK using Anderson's yet unused approach.
-The new plan starts when the mayor is abducted. He comes around in a remote shack, alone except for a black man(Badja Djola) wearing a mask similar to those used by the KKK in the film. Relating a story of how a young black man was castrated by the KKK, he implies the mayor will likewise be disfigured unless he talks by wielding a razor blade while relating the tale. In reality, the abductor is an FBI operative specially flown in. The mayor gives the names of those involved.
-Anderson uses the information to send fake invites to the involved KKK parties. They soon realize it's a setup and leave with out discussing the murders. The FBI, who are eavesdropping, home in on Lester Cowens, a jr. member of the outfit, as being nervous and not shutting up. He is later picked up by the FBI and driven around town to make it look like he is cooperating with the FBI. He is dropped off in a black community to give him time to "think" about stuff
-Anderson goes to a barbershop where Deputy Pell is getting a shave with a straight razor. He switches places with the barber and he nicks Pell with the razor. Anderson brutally beats Pell, for his role in the murders and assault of his wife. Ward, waiting outside, attempts to go in but is stopped by other FBI agents Anderson called in. Lester, nervous by now, is at home when his window is shot out. On the lawn is a burning cross. Cowens tries to flee in his truck but is caught by 3 hooded men who begin to hang him. He is rescued by the FBI, who chase the thugs away. The FBI now has evidence that can be used to find the murderers. They charge everyone involved with civil rights violations to ensure they'll be tried at the federal level. 4 of them had been convicted of a firebombing of a black man's home. Most are found guilty and receive 3-10 years.
-The film ends with a Sunday morning service on the site of a destroyed church attended by both white and black churchgoers.
- Gene Hackman as Agent Rupert Anderson
- Willem Dafoe as Agent Alan Ward
- Frances McDormand as Mrs. Pell
- Brad Dourif as Deputy Clinton Pell
- R. Lee Ermey as Mayor Tilman
- Gailard Sartain as Sheriff Ray Stuckey
- Stephen Tobolowsky as Clayton Townley
- Michael Rooker as Frank Bailey
- Pruitt Taylor Vince as Lester Cowens
- Badja Djola as Agent Monk
- Kevin Dunn as Agent Bird