On Fat Tuesday, Mardi Gras in New Orleans, ferry Sen. Alvin T. Stumpf is carrying hundreds of U.S. Navy sailors and their families from the Algiers dock to a celebration, when it explodes and sinks into the river, killing at least 543 on board. Special Agent Doug Carlin (Denzel Washington) from the Bureau of Alcohol, Tobacco, Firearms and Explosives (BATF) is sent to investigate the explosion and discovers evidence that the attack was committed by a domestic terrorist. On arrival at the scene he hears his ring tone; the ringing is coming from a body bag nearby. He then meets with the investigating police officers and FBI Special Agent Paul Pryzwarra, and informs them of his findings. Back at his office, Doug learns about a charred body pulled from the river, that of a Claire Kuchever. However, unlike the other bodies found in the river, this one was discovered to have been killed before the explosion.
Pryzwarra is impressed with Doug's detective expertise, and convinces him to join a newly formed government-funded detective unit whose first case is to investigate the explosion. With a team led by scientist Dr. Alexander Denny, they investigate the events leading up to the explosion by using a new program called "Snow White", which enables them to look into the past (4 days, 6 hours, 3 minutes, 45 seconds, 14.5 nanoseconds) in detail. The system is limited in that they can only see past events once; there is no fast forwarding or rewinding, although they can record what they see. Convinced that Claire is a vital link to the case, Doug persuades the team to focus on her. While investigating Claire's past through "Snow White", the bomber calls her to try and purchase her car to use to blow up the ferry. Although he decides not to purchase her car, during the phone call the "Snow White" team is able to discover an exact time and place where they know the terrorist will be.
Doug eventually discovers "Snow White" is actually a time window, and is also capable of sending inanimate objects into the past. Despite Denny's protests against tampering with the past, Doug has the team send a note back in time to inform his past self of the time and place to meet and stop the ferry bomber. Instead, his partner Larry Minuti sees it first and, while checking up on it, is shot by the terrorist through his car door. The team attempt to follow the terrorist, who takes Minuti with him, but he goes out of range of "Snow White", Doug then follows him in the present time using a "Snow White" like helmet that increases the range. Doug follows the terrorist to his home, after regaining consciousness, Minuti is shot again and burned. In need of a new car, the terrorist steals Claire's car and kidnaps her.
Using face recognition technology, the ferry bomber is identified and taken into custody. He turns out to be a disillusioned man named Carroll Oerstadt, who is angry at the U.S. government after being turned down for enlistment by the Marines and Army, who believed he was overcommitted and psychologically unstable. Convinced that the case is now closed, the government shuts down the "Snow White" unit's investigation. Despite the killer being caught, Claire and the ferry victims remain dead, which is unsettling to Doug considering the "Snow White" team presents an opportunity to alter history. Doug convinces Denny to do one last unauthorized experiment: send Doug to the past to save Claire and stop the ferry bombing. The procedure is risky, as until then no human had been sent through, and doing so could mean death to the time traveler. Against all odds, he survives the trip and stops Claire from being murdered in Oerstadt's house.
After tending to a bullet wound at Claire's house, Doug goes to the ferry where, with Claire's help, he kills Carroll, but is unable to disarm the bomb. To save everyone on the ferry, Doug and Claire drive the SUV with the bomb off the ferry into the water just before it explodes. Claire is able to escape, but Doug is unable to get out before the bomb explodes and dies in the underwater explosion. As Claire mourns Doug's death, she is approached by another Doug Carlin, the one from the present, who consoles her. As they drive off, the Beach Boys' song "Don't Worry Baby", which had played at the beginning of the film and at the end before they drive the car off the boat, plays on the radio.