An FBI counter-terrorism team and a black-ops agent are assigned to interrogate an American Muslim man named Yusuf (Sheen), formerly named Younger, who claims to have nuclear bombs planted in three U.S. cities that will go off if his (at first, unstated) demands are not met.
Using extreme torture as a method of interrogation, "H" (Samuel L. Jackson) attempts to force Yusuf to reveal the locations of the nuclear bombs. Also involved is Special Agent Helen Brody of the FBI (Moss) who, at the same time, is leading a team trying to locate the bombs using other information. Once H is authorized to interrogate Yusuf, he quickly shows his capability and cruelty by chopping off one of Yusuf's fingers with a small hatchet. Horrified, Special Agent Brody attempts to put a stop to the measures. Her superiors make it clear that the potentially disastrous consequences necessitate these extreme measures. As the plot unfolds, H escalates his methods (with Brody as the "good cop") and Yusuf, trained in resisting torture, maintains his silence.
When Brody accuses Yusuf of faking the bomb threat in order to make a point about the moral character of the United States government, he breaks down and agrees that it was all a ruse. He gives her an address to prove it, but visiting the address triggers a C-4 explosion at a nearby shopping mall, killing 53 people. Angry at the senseless deaths, Brody takes a scalpel and begins cutting Yusuf's chest. It is clear, though, that Yusuf is not afraid. He justifies the deaths by comparing them to the greater number of Muslim deaths by American hands. Yusuf then makes his demands: he would like the President of the United States to announce a cessation of support for puppet governments and dictatorships in Middle Eastern countries and a withdrawal of American troops from the Middle East. The group immediately dismisses the possibility of his demands being met, citing the United States' declared policy of not negotiating with terrorists.
H falters in his belief that the bombs' location will be revealed until the life of Yusuf's wife is threatened in front of him. Brody attempts to persuade her to cooperate, and she refuses. H. brings her in front of her husband and threatens to mutilate her in front of him. Brody and the others refuse to assent to her torture and start to remove her from the room. In desperation, H slashes her throat and she bleeds to death in front of Yusuf. Yusef still refuses to cooperate, and H tells the soldiers to bring in Yusuf's two children, a young boy and a girl. Outside of Yusuf's hearing, he assures everyone that he will not harm the children. H brings Yusef's children in front of him and prepares to torture the children. Brody demands that Yusef reveal the locations of the bombs. Yusuf finally breaks and gives three addresses in New York, Los Angeles and Dallas. H does not stop his preparations to torture the boy and girl and the others forcibly intervene and remove the children. H reminds the team of the amount of missing nuclear material Yusuf may have had at his disposal--some 15-18lbs were reported missing, with about 4-1/2lbs needed per nuclear weapon. H insists that Yusuf has not admitted anything about the existence of a fourth bomb. H insists that Yusef planned for the eventuality that he would finally capitulate to torture or coercion and reveal the three bombs' locations, and believes Yusef placed the fourth bomb for just such a contingency. When Brody refuses to retrieve the children for H, H unstraps Yusuf, saying Yusef has won. Yusef suddenly grabs one of the agent's revolver and kills himself. Brody walks out of the building with Yusuf's children. (This is the end of the original Direct-to-DVD version.)
In the extended version:
An FBI bomb disposal team arrives at one of the disclosed locations and resets the timer to prevent the bomb from going off. As the FBI are celebrating, the unknown fourth bomb is revealed behind a nearby crate as its timer counts down to zero. The screen cuts to black and the credits roll.