Three teens respond to an internet posting they believe is from a woman who is looking for sexual partners. After meeting the woman in her trailer, they find out that the ad was part of a trap. The ultra fundamentalist Five Points Church has been using the internet to lure in and then kill people whom it believes should be punished for their sinful lifestyles. A deputy sheriff investigating a car accident involving the boys is murdered by one of the church members. This prompts the local sheriff to call in the Bureau of Alcohol, Tobacco and Firearms. Agents led by Joseph Keenan (John Goodman) surround the compound and ask that the congregation peacefully surrender. The group's leader Abin Cooper (Michael Parks) responds by fatally shooting one of the agents. A gun battle then erupts between the two sides.
After significant losses on both sides (as well as the three teens), the gunfire stops when the booming sound of a trumpet fills the air. Believing it's a sign that The Rapture has come, Cooper's followers put down their weapons and come out of the compound.
At a confidential hearing, Keenan states that he took the church members into custody (in direct violation of a Supervisor's order to kill everyone to cover up the way the Bureau mishandled the situation). Instead of being reprimanded, Keenan is promoted to a position in the Bureau's Washington office. The government plans to use the Patriot Act to lock the congregation members away for the rest of their lives without a trial (since killing an American citizen in the name of religion fits the government's definition of "terrorism"). The trumpet sounds were not a sign of The Rapture but part of a prank that nearby Marijuana growers were playing on Cooper and his followers in retaliation for being harassed by them.
In the end, Cooper is shown pacing back and forth in his cell, singing hymns and waiting for The Rapture to come. A neighboring inmate yells at him to stop.
*In several interactive talks about the film, Director Kevin Smith has stated that the original ending called for The Rapture to occur after the trumpets sound. In that version, Keenan watched as Cooper, his congregation and the other agents all died when their hearts burst from their chests. The ground split open and Keenan saw the last agent killed by an angel dressed in armor. The angel glanced at Keenan, put a finger to his lips and said "Shhhh", then flew off into the sky just as the Four Horsemen of the Apocalypse descended.