In order to save the United States from mass destruction, ATF agent Ethan Carter (Dean Cain) must got undercover and join the Brotherhood of Liberty, a subversive militia group determined to overthrow the United States government. Headed by the passionate right-wing talk show host, George Armstrong Montgomery (Stacy Keach) the brotherhood plans to impliment an "new world order" for Montgomery's captive audience.
The militia has stolen three missiles whose warheads each contain enough anthrax to wipe out a city the size of Los Angeles. They are prepared to launch one of the missiles at the Air Force base where the President of the United States is giving a speech. The anthrax will kill everyone exposed within four days, enabling the brotherhood to take over. Agent Carter must work with his old nemisis and former militia member Wilson Fain (Fredric Forrest), who Carter put behind bars three years ago.
The ATF recruits Fain in order to get Carter "inside" the militia. Carter, who thinks he killed Fain's wife and son in the arrest three years prior, reluctantly agrees to work with Fain. Having just completed her ATF Training program, Julia Sanders (Jennifer Beals) is assigned to protect Carter. Following a successful infiltration, Carter learns that Fain's wife and son were not killed and have been placed in a witness protection program. Fain is cooperating in order to get his family back.
Having their suspicions confirmed the militia takes Carter and Fain hostage after they are caught breaking into Montgomery's headquarters. With the countdown already begun, Carter and Fain must rely on each other and Agent Sanders to destroy Montgomery and save the millions of lives in jeopardy.