The film tells the story of two siblings, Sam Cahill (Tobey Maguire) and younger brother Tommy (Jake Gyllenhaal). A Marine about to embark on his fourth tour of duty, Sam is a steadfast family man married to his high school sweetheart, Grace (Natalie Portman), with whom he has two young daughters, Isabelle and Maggie (Bailee Madison, Taylor Grace Geare). The film opens with Tommy being released from jail for armed robbery, not long before Sam departs for Afghanistan.

With Sam gone, Tommy attempts to redeem himself in the eyes of his family by wrangling old friends to help with kitchen repairs for Grace and the kids. As Grace slowly sheds her previous resentment towards her brother-in-law, news comes that Sam's helicopter has crashed over the water, leaving him presumed dead. In reality, he and a hometown friend, Private Joe Willis (Patrick Flueger), have been taken prisoner in a mountain village.

As months pass, Grace and Tommy bond over their mutual mourning, culminating in a passionate fireside kiss. They regret it afterward, and do not take this attraction any further, though Tommy continues to win the favor of his nieces.

Meanwhile, Sam and Joe are abused and tortured by militants, forced to make videotaped dismissals of the military and their mission, though only Joe cracks. The captors eventually deem him useless, forcing Sam at gunpoint to beat him to death with a lead pipe. Some time later, Sam is rescued.

He returns home, clearly traumatized by his experience. He drifts through encounters in a cold, paranoid daze, and refuses to explain what happened to his family. He also believes Tommy and Grace had a sexual relationship in his absence.

At Maggie's birthday party, a resentful and jealous Isabelle claims that Sam's paranoid assumptions are true: that Tommy and Grace have repeatedly slept together. That night, Sam snaps, destroying the newly remodeled kitchen and pulling a gun on Tommy. The police arrive, and after a frantic confrontation, Sam surrenders.

He is admitted to a sanitarium. During a visit from Grace, he finally admits to killing Joe, and they embrace. A letter between husband and wife is read in voice over, with Sam wondering if he will be able to continue living a normal life.