During a routine search of an enemy combatant Troy Barlow(Mark Wahlberg) and Conrad Vig(Spike Jonze) find a map lodged in an enemies ass crack, The map leads to secret enemy bases which contain stolen Kuwaiti gold bullion.
So Troy Barlow(Mark Wahlberg), Conrad Vig(Spike Jonze), Archie Gates(George Clooney), Chief Elgin(Ice Cube) set out to steal the gold for themselves.
After finding the gold and taking it for themselves they come across refugees that need help to get across the border to avoid being slaughtered by the Saddam's army.
They get to the border but are then stopped by American forces as they were AWOL and broke the peace core by killing Iraqi soldiers.
The three all agree to give the gold back in exchange for the refugees getting across the border

Stevens's mission in the Source Code is to assume the identity of Fentress, one of the train's passengers, locate the bomb, discover who detonated it, and report back to Goodwin to prevent the bomber from detonating a larger dirty nuclear device in downtown Chicago that is expected to happen, which could cause the deaths of millions of people. If this mission is successful, Stevens will save the lives of millions. Goodwin and the Source Code's creator, tell him that the Source Code is not a simulation, but a visit into the past in the form of an alternate reality. Goodwin assures Stevens that "everything will be OK." He's told that he cannot truly alter the past to save any of the passengers. He takes over Sean Fentress's body (a man who died on the train) in an alternate reality and lives the last eight minutes of his life. Through intel gathered from Goodwin, the bomber must have been in vision of the train to have been able to time the detonation the blow up train as it passed another.

Stevens is sent into the Source Code repeatedly, and each time a series of events repeat, with variations due to Stevens's acts. Meanwhile, he goes on searching for the terrorist and getting to know Christina, the woman who is sitting across from him, until the bomb that destroys the train goes off and Fentress dies, sending Stevens back to the chamber.

Rutledge and Goodwin urge Stevens of the severity of his mission, but with each time around he insists that someone tells him about his real-life personal situation. Stevens agrees to try and complete the mission with the added mission of saving Christina. But Goodwin continues to tell him that his actions can't alter the passed.

While going back and forth trying to spend each eight minutes finding out who the bomber is, he decides to spend one of the trips into the alternate reality to find more about his real-life personal situation. He borrows a cell phone from another passengers and learns that Air Force Pilot Colter Stevens died two months ago. He confronts Goodwin about this and she tells him that he had been shot down during the war, and his mutilated body was appropriated by the Air Force and used by Rutledge to operate the Source Code. Stevens then asks Rutledge and Goodwin to let him die, which they promise they will do once the mission is finished.

After multiple trips through the Source Code who finds the bomber. A young man named Derek Frost. He follows him off the train and finds that he has a white van in a parking lot by the train station that is strapped with explosives--the larger bomb everyone has been anticipating. After that trip in the Source Code he tells Goodwin the bombers name and the where the van with the larger bomb is located.

Now that the mission was a success, Rutledge orders Goodwin to erase Colter Stevens memory so they can use him for more Source Code missions to prevent more terrorist attacks. But Stevens persuades Goodwin to send him back one more time and give him one last chance to avert the train disaster. Goodwin agrees that he deserves to be allowed to die in peace afterwards instead of being held alive as a military brain in a vat. With the information he has uncovered from previous trips into the Source Code, Stevens is able to defuse the bomb and immobilize Frost before he can destroy the train.

Stevens and Christina kiss in the last seconds before the eight-minute mark. In that instant, Goodwin turns off his life support per his request, but to Stevens's surprise, his mind remains in Sean Fentress's body. He is then able to safely leave the train with Christina, also saving the rest of the passengers. Now in the alternate universe, an alternate version of Goodwin receives an email from Stevens explaining what has happened and that the Source Code can alter the target alternate reality. The movie ends with Stevens taking Fentress's place, and asking Goodwin to help Captain Colter Stevens and tell him that "everything will be OK.", which Goodwin had told Stevens earlier in the film.