A scene opening at a public building showing segregation of races with a water fountain for blacks and one for whites and a wooden country church burning with Mahalia Jackson's "Lead Me On" playing introducing the audience to the ugly reality of life in the rural south for most blacks during the Jim Crow era, which is being brought to a close in this movie.
Three young men, two whites and one black, are driving down a rural Mississippi road at twilight. They are James Chaney, Andrew Goodman, and Michael Schwerner, civil rights workers who in the summer of 1964 were working to get blacks voting rights in Philadelphia, Mississippi. Several vehicles tailgate them and one of them turns out to be a police car. An unseen police officer is supposedly going to issue a citation for speeding, but it turns out he and several KKK members murder the young men. Off screen, you hear gunshots of the men being murdered and the screen says "Mississippi, 1964".
FBI agents Ward and Anderson are driving to the fictional Jessup County, Mississippi (Neshoba County in reality) to investigate the missing men. Ward is a young, rather uptight, clean-cut, college-educated, and by the book agent and Anderson is a middle-aged, rough around the edges, and former small town Mississippi sheriff who believes in more experienced means to investigate, since he knows how the law works and how people's mentality is in the south. Both are liberal, but still don't see eye to eye.
The men arrive at the sheriff's department at the Jessup County courthouse and ask a young deputy to see the sheriff. The deputy blows them off and teases them, but the sheriff comes out of his office soon afterwards, He is a chubby, jovial, tobacco chewing, and generally personable man that accepts their invitation and into the office to talk. Initially he thinks they are there to solve racial problems under the direction of Martin Luther King.
Back in the car, Anderson and Ward are reviewing the sheriff's testimony to them about the three civil rights workers arrested for speeding, then released and escorted as far as the county line, never to be seen again. Ward is suspicious because the men are trained activists that are supposed to phone their headquarters every hour and that they did not do so after being released from jail or after their escort.
Anderson and Ward go into a crowded restaurant to have lunch that is segregated and Ward, not taking seriously the rules and customs of segregation, goes into the black section to question a young man eating lunch. The man refuses to comply and the whites at the front of the restaurant all stop eating and stare at them.
Anderson and Ward are at the remains of a black church in the countryside that was burned down where voter registration headquarters were being set up. The klan torched the place before anything could be done and the three missing men came back to apologize for what happened and talked to some locals. Ward wants to talk to some of them, but Anderson insists he's wasting his time that blacks refuse to do so in fear of retaliation, but Ward insists it's "bureau procedure". Ward questions an elderly black woman in a shack with her bedridden husband and the woman just answers yes sir and no sir to the questions he has about the incident of the burning.
At a house of a black family, three menacing white men knock on the door and a young boy answers it with the men asking to see the brother. He is the young black man at the restaurant that refused to talk to Ward. The two white men beat him mercilessly that he better not talk to the FBI agents.
Anderson and Ward are in their hotel room with Anderson going through the files of the missing young men. Ward does not understand where all the hatred of blacks is coming from. Anderson tells Ward a story of a black man that lived near his place when he was a kid that owned a mule that was later poisoned and the black man packed up and left. His father was a self-hating racist that had done it without any objection and taught his son that blacks will never be better than whites. Immediately afterwards, a shotgun blasts their window and there is a burning cross on the hotel property. Ward insists on more FBI agents being sent over, but Anderson objects to it thinking it will just cause more trouble.
Ward, Anderson, and numerous FBI agents set up an office at a local movie theater to rent for only $75 a month. At the same time, a Cadillac with a Confederate flag is pulling up at another building nearby and Anderson is sure it's the Grand Wizard of the KKK. Ward goes to do a license plate check on who the car belongs to. Anderson goes about his less traditional means to infiltrate and find out information. He goes into the local barber shop with the sheriff there. The town mayor is receiving a shave and introduces himself to Anderson that outsiders need to just let people live their lives in their community and not stir up trouble. The sheriff insists their community is peaceful and if the FBI agents continue to push them, there will be dead bodies. Anderson blows them off passive-aggressively that nobody is bold enough to stand up to the racism and that they are just there for a missing person's case.
Agent Bird is another FBI agent that comes to Ward and tells him the license plate does indeed belong to Clayton Townley, Grand Wizard of the KKK. And that a Choctaw Indian on a nearby reservation believes he found the car the three missing civil rights workers were in.
Anderson now goes into the local beauty shop flirting with the ladies that he wants a new hair job, then inquires who that vehicle belongs to and the local operator Mr.s Pell, states it belongs to Clayton Townley. Anderson confesses he's an FBI agent and Mrs. Pell is the deputy's wife. After questioning, a car squeals on the street and dumps a young black man out of it. He is the young black man at the diner that Ward tried to question. The sheriff tells the agents to back off and for he and his staff to handle the situation. Anderson reprimands Ward for speaking to a black man with a white audience and that this is what happens. They both already know Clayton Townley is the man that pulled up in the car and Ward explains to Anderson about the vehicle at the Choctaw reservation.
A Choctaw Indian man is filleting catfish and shows the FBI agents the vehicle. About a dozen of them all walk through the swamp in their nice suits and find it. A tow truck pulls the car out of the swamp. Anderson and Ward now realize they never left the state. Ward orders Bird to telephone asking for 100 men to search the swamp for the bodies. Once again, Anderson disagrees thinking it will just cause more trouble.
Over 100 Naval Reserve men have been activated to come search the swamp. During this time, black homes and churches are bombed and set on fire by klansmen and there is national media coverage with many white locals thinking the whole thing is a hoax set up by the FBI.
The media are interviewing Sheriff Stuckey and he insists the FBI are wasting their time searching for the three men and think the whole thing is a set up by the NAACP.
Ward and Anderson are back at the site where the black church was burned and a young black boy, Aaron is talking to a group of people about how the day will come that they will no longer have to kiss ass with the sheriff or any other powers that be. The other people leave, but Aaron and his father remain with Ward attempting to ask them questions. Anderson tries to as well, but Aaron speaks back at him that he knows there will be retaliation if they say anything and that they are not the law there and should be just as scared as they are.
Ward and Anderson go to Deputy Pell's home while he is on break from work eating dinner and watching a baseball game. The deputy is annoyed at them coming there, but Ward questions him about the night the three men were missing and Anderson converses with Mrs. Pell in the kitchen with her telling him the house they are in is where she was born and raised and about the hours her husband works. Afterwards, Ward and Anderson leave with Ward worried about Pell's confidence in the matter and that Anderson saw a wedding photo of the Pell couple with three men with the KKK symbol in the picture.
Anderson and Ward secretly spy on Pell escorting a drunk out of jail with Anderson using this as an opportunity to interview Mrs. Pell.
Anderson goes back to the Pell residence to question her brushing off Ward's college boy book smarts, gives her pretty flowers that smell bad, and she offers him iced tea while they talk. He tells her about his life growing up in Mississippi himself, hanging on to an unsuccessful marriage while working as an FBI agent, and questions her about Deputy Pell's alibi about 50 minutes he spent with her on the fateful night, but she answers a reluctant yes and he decides to leave.
At a black church, many locals have gathered from churches that have been burned down. A large group of klansmen are waiting outside the church to beat the people and run in horror after having seen them. Aaron is in that group, gets down on his knees to pray, and a klansman attacks him threatening to kill him if he talks to FBI agents again.
Back to the site of the swamp being searched, white locals are being interviewed by the press, some thinking blacks are treated badly and others thinking there's nothing wrong with the way they're being treated. The klansmen are teasing people searching the swamps for wanting to find them.
Back in town, the media are interviewing Clayton Townley. He's asked if he's with the KKK, but Townley insists he's a businessman and why people that are not white, Anglo-Saxon Christians are not accepted, among them including Jews, Catholics, Tartars, Mongols, Orientals, and Negroes.
Anderson goes into a local club that serves beer, even though he's in a dry state and attempts conversation with the men. Among them are Deputy Pell and several other men. Pell gives him a Falstaff beer to drink. He tells them of his days with bootlegged alcohol on his payroll and his days as a Mississippi sheriff, but they pay him no mind and Pell cuts him off and tells him they're not interested in his stories. Frank Bailey, a klansman that was seen at the beginning of the movie harassing and possibly killing the three missing civil rights workers, threatens and grabs Anderson that he and the staff of FBI are wasting their time trying to investigate and change things and that they need to leave unless they want more dead bodies. Anderson puts Frank in his place grabbing him by the genitals that they will not leave until the job is done. He thanks Pell for the beer and leaves.
Anderson is back at the makeshift FBI headquarters at the movie theater with a documentary about a klansman objecting to integration. Ward reprimands Anderson for his intimidation tactics and talking to the deputy's wife about the incident. Anderson is furious, but Ward reminds him that opening a can of worms happens on the inside.
There is a street protest in town with mostly blacks and some white participation. Anderson goes back into the beauty parlor with Mrs. Pell upset at the protest she sees outside.
Anderson and Ward stake out the sheriff's department on a young black man that's just been released from jail. Some klansmen pick him up in a truck afterwards with Anderson and Ward on their tail. They find the young black man in the woods castrated and Ward upset at what white people inflict on blacks there.
Ward goes up to the Walker residence, the parents of the young black man pleading for them to press charges and they refuse to talk.
Ward and Anderson are convinced the sheriff's department arranged the murder of the civil rights workers and once again back in town interviewing Deputy Pell if he's a member of the KKK or had the three men murdered and he denies the allegations. Afterwards, he leaves with the sheriff reassuring him, ignoring the media, and Frank Bailey violently attacks the media to get out and leave them alone. The mayor confronts Ward and Anderson and is extremely frustrated at the FBI's tactics on his community, but Ward and Anderson insist they will not back down.
Mrs. Pell is arriving at her home from grocery shopping and sees Anderson in another vehicle watching her. She is troubled at this and feels he knows something she knows.
A group of klansmen firebomb a home of a black family with a boy as a witness as to who the men were. The FBI agents decide to give the boy a box to put over his head to disguise him.
The accused men are in court with a lenient judge insisting it's the agitation of the FBI agents that led to the men bombing the home of the black family. He gives them a suspended five year sentence with the men celebrating.
That night, there is riot in a black neighborhood with Anderson and Ward coming there and the sheriff refusing to let them in to stop it.
The home of Aaron and his family is being invaded by klansmen and torched on fire. The wife and girls are told to leave and go up the road. Aaron's father brandishes a rifle for the men to come out, but before he can do anything, he's clubbed over the head and left to hang by Frank Bailey. Aaron rescues his father.
The next morning, there is the aftermath of the fire and dead livestock burning. Anderson tells Ward what is happening is progress, but Ward feels all they have done is cause trouble. Aaron and his family have been asked to go live in Detroit with other family members. Ward reminds Anderson the three workers are still missing and he now needs to break the alibi Mrs. Pell told him about the 50 minutes with her husband.
Clayton Townley is giving a speech at a klan rally that night at how much he loves Mississippi and that federal powers that be coming to their state will not change their ways for the better. A large group of unattractive inbred locals cheer him on. Ward and other FBI agents are taking down license plate numbers of cars of those attending and Deputy Pell confronts him that they have no business there, but Ward insists it's a KKK meeting.
Anderson is back in town and goes to visit Mrs. Pell who is now closing down the beauty shop for the day. She reluctantly lets him in and tells him he needs to leave because it's so ugly at what she and many other white people have to live with, since most of the rest of the country see them as nothing but bigots and racists. She's upset enough at it that she spills her guts to Anderson confessing that her husband was one of the people that was out that night killing the civil rights workers and that they buried their bodies on a farm in an earthen dam.
The FBI agents have unearthed the bodies of the three men and they are taken to the local morgue for an autopsy, with the FBI and sheriff's department refusing to comment on the incident. The sheriff pulls Pell to the side and tells him to take care of business at home, with Pell having initially failing to realize his wife released the information.
Mrs. Pell is at her home watching television with her husband, Frank Bailey, Lester Cowens, and Wesley Cooke arriving at the home as witnesses. Pell attacks his wife and beats her within an inch of her life for releasing the information.
Ward gets word at headquarters that Mrs. Pell has been badly beaten and in the hospital. He orders agents to secure the area and for Anderson to come down, with Anderson not aware at what's happened. Anderson comes into Mrs. Pell's room to see her on life support and Ward sitting down. Infuriated, Anderson wants to take matters into his own hands. He and Ward end up fighting with Ward pulling a gun on him, but now Ward agrees that his ways have been hopeless and that he wants justice to be done Anderson's way and do whatever it takes to apprehend the men.
A funeral is now being held for James Chaney and the two white men with the black pastor of an ornate church giving a speech enraged at the injustice being done to blacks in his community, the hypocrisy, and how the locals continue to let it happen. Numerous FBI agents being brought in from outside also attend the graveside services and go to work to help solve the case and justice be done.
The mayor is about to get in his car and is kidnapped by an unknown man. He's taken to an abandoned shack in the country with the hooded man that kidnapped him revealing himself to be a supposedly local black man. The black man tells the mayor a story of a young black man that was castrated by whites for doing nothing more than being a negro. He takes the mayor's pants down and threatens to castrate him if he doesn't tell him who killed the three civil rights workers and what happened. The mayor decides to comply.
The black man gets inside a small commuter airplane on a farm and takes off in a rainstorm. He is revealed to be a "specialist" by the FBI from Agent Anderson. Anderson assures Ward the mayor won't talk and would be killed if he did so. It turns out that Deputy Pell and Frank Bailey did the killing and that Clayton Townley engineered it. But Ward knows that local charges can never be brought on the men and it would have to be federal. They squabble again about their illegal means to get information, but decide to follow through.
Clayton Townley pulls up to a church not understanding what's going on. The sheriff, Deputy Pell, Lester Cowens, Wesley Cooke, and Floyd Swilley are all in the church assuming Townley called a meeting for them. Lester is confounded telling him he had a note written to him to meet there and that they must be set up, but Townley tells him to shut up and for all the men to leave the place quietly. Ward and Anderson are listening to a tape of the men in the church.
Anderson and another FBI agent go into a footwear repair shop Lester works at with Anderson teasing him about a ride. Lester is confused at this and the other agent tells him to get in the car with them.
Lester is being driven around with other FBI agents that they know all about his involvement with the night of the three missing civil rights workers, but he refuses to talk. He's told by Anderson to go on record to save himself trouble. They drop him off in the middle of a black neighborhood with residents glaring at him and he runs off.
Deputy Pell is receiving a shave at the barber shop with Anderson taking over for the barber to shave Pell. He harasses him and cuts his face telling him about the night of the killings and berates him for what he's done, throwing him around the place.
Lester and his wife and baby are having dinner that night and a gunshot blows out the window of his home. He sees a burning cross on his lawn and tries to escape, but the klansmen kidnap him. They take him out and tie him to a tree with him pleading he didn't say anything and the FBI come to his rescue for him to turn himself in. It turns out the klansmen are FBI agents in disguise that played a charade.
Anderson and the other FBI agents arrest Deputy Pell, Sheriff Stuckey, Frank Bailey, Floyd Swilley, Wesley Cooke, and Clayton Townley. With the exception of the sheriff, all the others, including Lester, receive sentences ranging from anywhere from 3 to 10 years.
The mayor has hung himself because of the guilt from what he let happen and that he was supposedly subpoenaed to testify in court. Ward and Bird remove his body with Bird questioning why he did it and Ward insists he was guilty for letting all this happen, but maybe the FBI agents are guilty as well.
Anderson goes back to the Pell residence to visit Mrs. Pell, whose home was supposedly trashed out by the klansmen. He apologizes to her for what happened, but she knows she did the right thing and intends to remain in her home for life.
Anderson and Ward are at the cemetery with a black female gospel singer with an interracial group wanting to join and all be one. Things seem to be getting better, but we're taken to the gravestone of James Chaney, which has been destroyed.