Gyllenhaal plays Coulter Stevens, a helicopter pilot whose last memory is being shot down in Iraq. He wakes up on a train in front of a beautiful stranger (Michelle Monaghan), who calls him Sean Fentress. Confused and disoriented, Coulter stumbles around the train trying to get his bearings, only to have the train blow up eight minutes later, killing him and everyone on board. Coulter wakes up again, this time in a cold, mechanical chamber, strapped into a chair, with a computer screen in front of him and a woman on it, trying to get his attention. After some debate, she identifies herself as Goodwin (Vera Farmiga), and informs him he is participating in "source code", a futuristic device that allows Coulter's consciousness to be dropped into Sean's body. A terrorist bombed the train, saying downtown Chicago was next, and Coulter has those eight minutes to determine who the bomber is and stop him.

Like Rockwell's Moon character Sam Bell, the nature of the source code program detaches Coulter from his sense of self. During the first few runs through the program, he becomes obsessed with contacting his father and finding out more about the program, which he has to do within the confines of the "source code". Without delving too far into spoilers, the "machine" Coulter finds himself in after every explosion is revealed to be nothing more than an imagined space inside Coulter's consciousness. Bizarrely, the hero of Source Code is almost never "real", in the sense that the train sequences are merely Coulter's projection and sense of himself, and the scenes inside the device are imaginary.

In a somewhat ironic twist, however, Jones betrays the screenplay by Ben Ripley, which is, despite its clever hook, mostly written like an action movie. It's really hard to begrudge a director for taking on a thriller and insistently adding ideas and themes to it, but the sequences in which Coulter searches for the culprit feel cursory and lacking in tension. Most of this can be chalked up to the script, which provides a laundry list of characters that are just overwritten, each one so suspicious and suspect that they can't possibly be the bomber. The film devotes entire sequences to Coulter picking and tracking a suspect (in rather unfriendly, intrusive ways), yet the viewer can hear the "false alarm" bell ringing before Coulter even settles on a particular target.

Gyllenhaal gives a solid performance, allowing the character's anger and irritability to flare up without turning Coulter into a wholly unlikable person. With each return journey into "source code", Coulter becomes more and more infatuated with the woman he keeps waking up in front of, determined to save her and the other 800-plus passengers. The inventor of the program (a poorly-utilized Jeffrey Wright) claims it isn't possible, but Coulter doesn't want to hear it. The film works itself out in a way that will inspire debate and discussion among viewers, and leaves them thinking about the ideas and concepts contained within. It's funny to say, but no less true: if only the part with the ticking time bomb were equally interesting.