Captain Colter Stevens is a decorated airman who awakens in the body of a man called Sean Fentress inside a train in Chicago, where he meets a woman called Christina. Before he can understand what is happening, a bomb goes off and destroys the train. Stevens awakens inside a chamber, where he is greeted through a computer screen by Colleen Goodwin, a military woman who tells Stevens that he is inside the Source Code, a program that allows him to take over the body of a person in the last eight minutes of this person's life. Earlier that day, a bomb exploded and destroyed a train in Chicago. Stevens' mission is to locate the bomb and discover who created it before another bomb, this time a nuclear device, detonates somewhere in Chicago, causing the death of millions of people. Stevens is sent back to the train, where he encounters the bomb, which is activated by a cell phone, at the ventilation shaft of the bathroom. It explodes again, and Stevens returns to the chamber, where Goodwin and the Source Code's creator, Dr. Rutledge, tell him that the Source Code is merely a simulation and that Stevens cannot alter the past and save Christina, with whom he has grown attached to. Stevens suspects that Goodwin is lying to him about him having been recruited during a trip to Afghanistan and spending two months in Source Code training. Stevens is sent back several other times, in which he retrieves a gun from a the conductor's compartment on the train and eventually discovers that the bomber is an American extremist called Derek Frost. Stevens is able to inform Goodwin of this and confront Frost before he activates the second bomb. The Army, having received the information from Goodwin, captures Frost and saves Chicago. However, the train is still destroyed and Christina is still dead. Investigating Goodwin's rank based on a glimpse of her insignia which he caught during his debriefing, Stevens discovers that he died in the war and his body was apprehended by the Army and used by Rutledge to enter the Source Code, as Stevens is the only soldier with the mental and psychological faculties able to withstand the burden of the such a mission. After listening to his father's declaration about him, Stevens makes Goodwin, who has become disgusted by Rutledge's ruthless ways, give him one last chance to save Christina and the train's passengers before she pulls the plug on him against Rutledge's orders. She relents. With the information he has uncovered from previous times, Stevens is able to defuse the bomb and capture Frost before he explodes the train. Frost is arrested by the police and the people of the train are saved. Stevens and Christina kiss in their last seconds, but, much to his surprise, he doesn't return to the chamber after the eight minutes have passed. As it turns out, when Goodwin pulled the plug, Stevens' mind remained in Sean Fentress' body. Having received a second chance to lead a normal and happy life with Christina, Stevens - now in Fentress' body - leaves with her. Meanwhile, at the Nellis Air Base, Goodwin discovers that, unlike Rutledge's previous affirmations, the Source Code's activation does lead to the creation of new timelines due to the manipulation of Quantum Physics, and that, in the new timeline created by Stevens' actions, there is another Colter Stevens, still being kept alive by Life Support, awaiting to be activated for his first Source Code mission, as the train disaster never happened.
