Colter Stevens, a decorated army helicopter pilot, wakes up in the body of an unknown man on a commuter train heading to Chicago. Disoriented and confused, he discovers he is part of an experimental government program called the Source Code, which allows him to cross over into another man's identity within the last eight minutes of his life. With the train set to explode from a terrorist bombing, Stevens' mission is to locate the bomb and identify the bomber to prevent a much deadlier second attack. Guided by officer Carol Goodwin through a digital communication link and overseen by the program's creator, Dr. Rutledge, Stevens must navigate the puzzling world of the same eight minutes repeatedly, gathering clues and piecing together the puzzle with each iteration.

As Stevens delves deeper into the repeating eight-minute segments, he becomes close to one of the train's passengers, Christina Warren, and starts to form a connection with her. He questions the morality and purpose of his mission, grappling with his own identity and the implications of the Source Code program. His determination to alter the tragic outcome grows with each successive loop, but the constraints of his reality, the fleeting timeframe, and the perplexing layers of his task weigh on him. Each return to the Source Code reveals new facets of the enigma, challenging Stevens to unravel the complex web of events before time runs out.