Set in an unnamed southwestern small town, while on the way to high school, Travis (Michael Angarano) notices members of the Five Points Church (a thinly veiled version of the Kansas hate-mongering Westboro Baptist Church), led by Abin Cooper (Michael Parks), a middle-aged David Koresh-esq leader (also loosely based on WBC leader and fanatic Fred Phelps), protesting the funeral of a local gay teenager who was found murdered; the third hate crime murder in a month. During Travis's first class, his teacher talks about how Cooper and his church had their town ridiculed for his racial actions and beliefs. Later, Jared (Kyle Gallner), a friend of Travis, reveals he received an invitation from a woman he met on a sex site for group sex with himself, Travis and Billy Ray (Nicholas Braun). They borrow Travis's parents' car and travel out into the country to meet with the woman.
Along the way, they accidentally sideswipe the vehicle of Sheriff Wynan (Stephen Root), while he was engaged in a homosexual affair in his car. Afraid, the boys drive off. Sheriff Wynan returns to the station and tells his deputy Pete (Matt L. Jones) to go and look for the vehicle (but doesn't tell him about what he was doing out on the back road).
Meanwhile, the boys arrive at the trailer of the woman who sent out the invitation, Sarah Cooper (Melissa Leo). She encourages them to drink, and after being drugged by the beer, they pass out while undressing. Jared wakes up while being moved in a covered cage. He realizes he is in the sanctuary at Five Points after he identifies Cooper. Here, Cooper begins a long, hate-filled sermon/monologue before his warped followers about sin reeks in the world and that all evil must be eradicated before the end of the world comes which is their one-way ticket into Heaven. Cooper then identifies another captive, a homosexual young man they lured in through an internet chat room. They bind him to a cross using saran wrap and violently execute him with a revolver and drop him into a small crawl space where Travis and Billy Ray are bound together; thus revealing that the Five Points Church is responsible for all the hate crimes and murders throughout the entire state.
Cooper then begins binding Jared to the cross to have him executed too, but stops when he notices Deputy Pete driving up to the church. Cooper goes outside and talks with Pete at the front gate of the Five Points compound where Pete explains that he is looking for a hit-and-run driver who sideswiped Sheriff Wynan's car earlier that night. Cooper denies knowing anything about the hit-and-run accident or if he has seen any particular car as described by the sheriff. But Pete soon realizes that Cooper is lying when he sees the car within the church compound partly covered with a tarp.
In the hole, Travis and Billy Ray use a protruding bone from the corpse to cut themselves free, which is heard by Caleb (Ralph Garman), one of Cooper's henchmen. He lifts up the trap door just in time to see Billy Ray escape and begins chasing after him. Billy Ray is not able to help Travis out of his tight saran wrap cuffs and leaves him for dead. Caleb chases Billy Ray while passing Travis into a room stocked with weapons, where the two end up shooting and killing each other. Pete hears the gunshots and calls Wynan for back-up, but is shot and killed by Mordechai (James Parks), another one of Cooper's henchmen. Cooper then blackmails Wynan over the CB radio, telling him to stay away or he will reveal Wynan's homosexuality to his wife and the whole homophobic small town. In despair, Wynan calls the local ATF whom put him in touch with Agent Joseph Keenan (John Goodman), who begins setting up outside of the church.
At dawn, while the Cooper family mourns for Caleb, Travis (who had broken free and feigned death alongside Billy Ray's corpse) arms himself with a rifle and makes a run for it, eventually making it outside where he is shot and killed by Wynan, who mistook him for a member of the congregation. Wynman (clearly insane at this point out of fear of his closeted homosexuality being outed) demands that the ATF launch an attack on the Five Points compound and kill everyone (so that the secret of his gay life will not be revealed), but Agent Keenan refuses and orders him to be confided to his police car.
A Branch-Davidian stand-off occurs as Agent Keenan tries to reason with the family to come out of the compound and surrender for they have a warrant for Cooper's arrests for numerous firearms violations. But Cooper himself appears at a window and shoots and kills Agent Brooks (Kevin Pollak), one of Keenan's men, by shooting him in the head with a hunting rifle. A huge and violent shoot-out begins as the Five Points fanatics, armed with AK-47 automatic rifles and TEC-9 sub-machine guns, open fire on the ATF agents who return fire with their AR-15 rifles and 9mm sub-machine guns. There are some casualties on both sides. Sheriff Wynan is one of the fatalities when bullets from the entrenched fanatics riddle his police car.
In the midst of the shooting, Agent Keenan receives a phone call from ATF higher-ups ordering him to start a full raid of the complex to ensure that no witnesses remain of the operation, and no one can tell the press of their mess up. Another tactical agent named "Harry" (Kevin Alejandro) struggles with this decision and argues with Keenan in private against doing this. Keenan coldly dismisses Harry's protests for personal reasons -- rationalizing his decision based on personal gain and the reputation of the ATF -- and Harry storms off in disgust.
During the shoot-out, a teenage cult member named Cheyenne (Kerry Bishé) attempts to escape from the compound, but is captured by an ATF sniper (Mark Blucas) who tries to reason with her to give up. When the ATF agent hears over his com-link about the order to kill everyone inside the compound, he points his rifle at her but gets killed by Sarah, whom is Cheyenne's mother. Sarah drags Cheyenne back inside the building and orders her to stay put for they they all will die soon and be accepted into Heaven.
During another lull in the shoot-out, Cheyenne unbinds Jared, begging him to help her hide the children. Jared coldly refuses due to the fact that the Five Points Church is evil and had killed both his best friends as well as countless other people over the past several years, and the argument turns into a fight. Sarah notices them and attacks Jared. Cheyenne tries to break up the fight and accidentally shoots Sarah in the process, killing her. Jared, realizing no matter what he does he will end up dead, helps Cheyenne hide the children in the attic of the compound. In the meantime, Keenan and his men manage to break down the main gate to the compound using an armored truck as a battering ram, and the agents swarm into the compound.
Cheyenne and Jared run outside to plead with Keenan to spare the children but are both brutally shot and murdered by Tactical Agent Harry, who has come around to accepting Keenan's rationales though Keenan is now visibly disturbed the reality of this outcome and Harry's actions. The shoot-out is then suddenly interrupted when a mysterious loud trumpet ominously blast echoes across the sky.
The remaining Coopers lower their weapons and run outside, rejoicing, claiming that "the rapture" has come upon them as the trumpet continues to blast. A very pleased Abin Cooper calmly approaches a very stunned Keenan and confidently taunts him that God's wrath is upon them. He raises his arms and stands in the face of a confused and worried Keenan in a moment of triumph, daring him to defy God as the trumpets blare.
Several days later, during a briefing before high-ranking government officials, Keenan is asked what he did next and he reports that he then head-butted Cooper and took the rest of the congregation into custody. He explains that the trumpet noises were not in fact the rapture but came from a group of marijuana farmers who lived down the road and were irritated with Cooper. As a prank they rigged up an old fire truck siren to an MP3 player with loud trumpet noises, unaware of the shootout taking place over the hill. Keenan is promoted despite disobeying a direct order from his superiors at the time to kill everyone at the compound. Keenan is surprised that he is not punished for his insubordinate actions but his superiors explained that their initial decision to kill the members of the congregation was mostly personal anyways and that they are satisfied with the alternative punishment of taking away the prisoners constitutional rights to due process, locking them up without ever letting them go to trial. They also laugh at the irony that Abin, who views homosexuality as an abomination, will more than likely be raped numerous times by his fellow male inmates. Keenan laments this outcome in a story he shares about a couple of hungry brawling dogs he once knew that taught him about the darker side of human nature and the way simple beliefs can turn humans into bloodthirsty animals.
In the final scene, Abin Cooper is seen locked in a jail cell in a Federal prison in solitary confinement, where he spends his time pacing anxiously around his cell muttering like a madman -- singing and preaching to himself -- occasionally being told to "shut up" by other prisoners.