On November 1, 2004, Hank Deerfield (Tommy Lee Jones), a gravel trucker and a retired military police sergeant, receives the unsettling news that his son Mike (Jonathan Tucker), a soldier recently back from Iraq, has gone missing. Hank, who lives in Tennessee with his wife Joan (Susan Sarandon), immediately drives to Mike's base in New Mexico to launch his own search. Before leaving, Hank assists a school custodian in raising the American flag correctly, showcasing his values.
Upon arriving at Fort Rudd, Hank meets Sergeant First Class Dan Carnelli (James Franco) and goes through his son's belongings, secretly taking Mike's cell phone. As he reviews the corrupted video files with the help of a hacker, he tries to file a missing person's report with Detective Emily Sanders (Charlize Theron), but finds himself hampered by procedure and an uncooperative police department. Emily faces her own struggles as she deals with male colleagues who belittle her for being a woman and voicing opinions in a male-dominated homicide unit.
After a gruesome discovery of Mike's burned and dismembered body, it becomes clear that the military believes his death is drug-related, particularly with the evidence found near his remains. Hank persuades Emily to investigate the crime scene, where they uncover discrepancies regarding the color of a vehicle seen near the murder. Although the Military Police claim jurisdiction, Hank feels the army is intent on protecting its own, thereby complicating the investigation.
Emily invites Hank to dinner, where he recounts to her son the Biblical tale of David versus Goliath, an apt metaphor for his ongoing quest for the truth. When a bartender named Eve (Frances Fisher) identifies Mike's squad mate CPL Steve Penning (Wes Chatham), new leads come to light about the night of Mike's death. Through a series of interviews, Hank and Emily discover that Mike had been drinking and socializing with his squad just before tragedy struck.
Despite growing evidence pointing to his son’s comrades as potential perpetrators, Hank struggles to believe that his son's fellow soldiers could take such treacherous actions against him. As frustrating truths unfold, such as the discovery of an AWOL soldier with ties to the case, Hank takes matters into his own hands, confronting suspects and piecing together Mike's last hours.
Eventually, the investigation leads to a shocking climax. Bonner (Jake McLaughlin) is found dead under suspicious circumstances, intensifying the scrutiny on Mike’s squad. Through smart detective work, Emily aptly connects the pieces of the puzzle, revealing that Mike was indeed murdered by his comrades in a senseless act of violence. As more confessions come to light, Penning admits to the stabbing, providing heartbreaking implications about the nature of their military camaraderie.
Haunted by regrets and memories of his son, Hank reflects on their last conversation—one that will linger with him indefinitely. As he collects Mike's belongings, he faces Ortiz and acknowledges the turmoil both he and the military endure. The story culminates in an emotionally charged moment as Hank returns home, only to discover that Joan has opened Mike's last package, revealing a photograph of his squad, along with an American flag. In a poignant tribute, Hank flies his son's flag upside down at the local school, signaling distress and honoring Mike's tragic fate.
