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Captain Colter Stevens (Jake Gyllenhaal) wakes up on a train on route to Chicago with no recollection as to how he got on board. Christina (Michelle Monahan) says that she took his advice and that it was good advice. Stevens is alarmed and doesn’t know what is going on. He explains to her that he is a soldier and tells her his name but she refers to him as Sean Fentress and asks what is going on. A soda can is cracked open and a woman carrying coffee spills some on his shoe. Christina’s phone goes off – her ex-boyfriend Bryan calling her, which he didn’t really do when they were together. The conductor comes around asking for tickets and Stevens doesn’t know where his ticket is. Christina reaches into his breast pocket and gets it for him, curious about her friend’s mysterious behavior. The train stops at a station and Stevens watches as a business man complains, a college student bumps into a woman carrying papers and picks them up, while another person finds a man’s wallet and returns it to him as he leaves the train. Stevens gets up to go to the bathroom and regain his bearings and looks in a mirror, but it’s not his face staring back at himself – he is in another man’s body. Stevens freaks out and leaves the bathroom and Christina tries to sort him out when a bomb explodes and everyone on the train is killed.

Stevens wakes up in a harness in a weirdly constructed chamber. In the darkness he can see a computer screen where Carol Goodwin (Vera Farmiga) asks if he was able to ascertain the whereabouts of the bomb. Stevens doesn’t recognize her and demands to know what is going on. He is confused and tells her that the only thing he remembers is being in Afghanistan with his unit and doesn’t recognize her. Goodwin is mildly surprised and tells him that he’s been training for the Source Code Program for the last two months. Goodwin plays a string of “memory threads” – lines Stevens was made to memorize as part of the program – until Stevens memory is restored. He asks about his mission and if his father knows he’s stateside but Goodwin doesn’t give him more information: she tells him that time is running out and he should focus on locating the bomb on his next attempt.

Stevens awakes in the program again. He believes he is in a simulation, so when Christina starts talking to him, he calls her the Pretty Girl, the distraction of all simulations. Christina is both flattered and confused. Stevens gets coffee spilt on his shoe again and begins talking to himself. Christina begins reacting to his behavior differently, which causes him to realize that even though it’s the same train…it’s somehow different. He remembers that the bomb blast came from immediately behind him. He goes to the bathroom and waits for a sickly Middle Eastern man to leave the bathroom. He looks around and checks the air vent, locating the bomb which is connected to a cell phone trigger. He talks to Goodwin and asks her if he is supposed to diffuse it and asks her what to do. When he gets no response he gets frustrated and leaves it, accepting that it’s going to go off. He leaves the bathroom and pretends to be a transit cop, telling everyone to turn off their phones and electronic devices. He encounters a day trader who doesn’t want to listen, so Stevens breaks his jaw. Christina freaks out, along with most of the passengers right before the bomb explodes.

Stevens wakes up in the Chamber. Goodwin asks him if he located the bomb and Stevens tells her that it is in a vent in the bathroom. Goodwin is pleased but tells him when he goes back in, he will need to locate the terrorist. The supervisor of program, Dr. Rutledge (Jeffrey Wright) tells Stevens that he needs to focus on the mission. Stevens complains about the state of the Chamber since it is leaking and very cold. Rutledge is amused by Stevens’ description of the Chamber and tells him that it’s not their concern. Stevens demands more information and Goodwin asks Rutledge if she can tell him more. Rutledge tells her that she can.

Goodwin explains that earlier that day a Chicago commuter train was blown up in a terrorist attack. Stevens is using the Source Code program to enter the last eight minutes of victim Sean Fentress’ life in order to see what happened. Stevens is confused but doesn’t get to ask any more questions as he is thrust back into the program.

Stevens wakes up on the train and converses with Christina for a few minutes. He learns that she quit her job and signed up for an LSAT class and will eventually move to India and become a guru (jokingly). Stevens moves his foot and the coffee is spilt on Christina’s foot. She shrugs it off which impresses Stevens. He tells her that she’s a kind person. The conductor comes and Stevens asks if he has seen anyone suspicious and the conductor blows him off. He asks Christina about everyone on the train in the form of a game. She enjoys it until Stevens focuses on the Middle Eastern guy entering the bathroom. She tells him that he’s racially profiling people now and Stevens asks her if she’s seen anyone else enter the bathroom. She tells him that he went to the bathroom, which causes Stevens to freak a bit and rummage through his stuff, looking for signs that he might be the terrorist. He finds nothing. When the train pulls into the station he asks Christina to get coffee with him and leave the train. She is hesitant but Stevens tells her he has a bad feeling about staying on the train and kisses her passionately. They get off at the station and Stevens has her sit down and wait as he follows the Middle Eastern man looking for cell phone use. He assaults him on the tracks for the phone. The bomb goes off regardless and the Middle Eastern man pushes him onto the tracks where he is hit by the 7:45 train.

Stevens wakes up back in the Chamber. He tells Goodwin that he saved Christina. Goodwin is confused and explains that it couldn’t have happened. Rutledge explains that Source Code is basically a computer program which utilizes Quantum Mechanics to simulate an altered event. Anything Stevens does cannot affect the primary time line; he can only use the pieces he has at his disposal to figure out what happened.  Stevens gets frustrated and asks Goodwin if she’s ever been in the Source Code. Goodwin says no since she doesn’t meet the requirements of the program. Stevens asks what the requirements are but he doesn’t get a straight answer. She tells him that there is a gun in a lockbox on the second level of the train and that he should go for it.

Stevens is back on the train. He asks Christina if she knows him well enough to trust him if he were to do something crazy or dangerous. Christina says no. Stevens laughs at her blunt honesty. He goes for the lockbox on the second level when he thinks the conductor isn’t looking. He takes a flashlight and uses it to break the door handle and the lock on the box, stealing the gun. However, he is ambushed by the conductor and a guard who knock him out. The conductor cuffs him on the first floor. Stevens comes to with a minute to spare with Christina asking him what is going on. He asks her what she would do if she had less than a minute to live and she tells him she doesn’t know. He is silent for a moment and tells Christina he would tell his father that he loves him and wishes they had left each other on better terms. The bomb explodes with her telling him that it will all be ok.

Stevens comes up empty handed again, frustrating Goodwin and Rutledge. They tell him that he needs to focus because there will be a second attack. Stevens is alarmed when Rutledge explains that the train bomb was a warning: there is another bomb heading to Chicago with a nuclear device attached. He asks who he’s working for and for more information on the program but is given nothing. Goodwin shifts over to ask Rutledge a question exposing a military insignia which Stevens memorizes.

Stevens is sent back in. He tells Christina about a friend he served with in the military named “Colter Stevens.” He tells her that he doesn’t know what happened to him so he sends Christina on a mission to look it up while he goes to take care of some business. He draws out the insignia and then notices a man sitting next to the college kid. He goes over and intimidates him and searches his bag forcefully. He finds nothing and is disappointed. He notices a woman with a Walter Reed medical bag on the second level and goes up to talk to her. He asks her if she recognizes the logo and she does, telling him it is an Airbase in Nellis. He thanks her and offers her money to borrow her phone. She lends it to him and Stevens uses it to call Rutledge at Nellis but he is interrupted by Christina who has bad news: She looked up Colter Stevens and learned that he died two months prior in Afghanistan. Stevens is in shock at the news and lets time run out on this try.

Stevens wakes up in the Chamber. He tells Goodwin that he heard a news report of his father speaking about his death and Goodwin is truly surprised. He asks if he is dead and Rutledge cruelly confirms that he is serving his country from beyond the grave as he is the only one that Source Code may work for. Stevens is disgusted. The Chamber’s properties begin changing and expanding, reflecting his mental state. It breaks down as Stevens’ psyche begins to deteriorate. Goodwin has him pull it together and tells him that even though he’s dead he can still save lives. Stevens demands that he be taken off of life support if he completes the mission. Rutledge agrees: If Stevens can prevent the next attack, he will be released. But Rutledge doesn’t think Goodwin is pushing Stevens hard enough. He forces Stevens to go through three more simulations before playing a clip of his father (the voice of Scott Bakula) talking about Stevens’ death. This motivates Stevens for his next run.

Stevens wakes up. He goes for the gun again and successfully gets it. He gets the cell phone from the bomb, praying it won’t explode when he pulls it. He makes a call and the person who picks up appears to be the guy he harassed in the last attempt. He pulls a gun on him and makes the man slide over. The man tells him to call the phone again and he does: it isn’t this man’s phone. Stevens apologizes and goes after the real target: the man who dropped his wallet. Stevens gets off the train and follows him, seeing him toss his wallet onto the next compartment. He climbs aboard and sees an ID: Derek Frost. The train begins moving again and Stevens pulls the emergency Door handle, jumping off the moving train. Christina sees this and demands the train be stopped. Stevens goes after Derek and corners him by his van. Derek shows him the nuclear bomb and explains that not many people could have done it. Christina calls out to Stevens and distracts him long enough for Derek to pull a gun on him and shoot him. Derek then shoots Christina. As both lay dying on the ground, the train explodes in the background. Stevens asks Derek why he’s doing this. Derek tells him the world is hell and the only way to fix it is by starting over in the rubble. Derek drives off, and Stevens tells Christina that everything is going to be ok even though she’s already dead.

Stevens tells Rutledge and Goodwin that the man they want is Derek Frost and provides them with the license plate of his van. They send out this info and the military successfully apprehend Frost, preventing the bomb from going off. Stevens requests that before he be shut off he be allowed one last attempt to save everyone on the train. Rutledge says no and goes off to celebrate the vindication of the Source Code program and brag about its success. Stevens talks to Goodwin and asks her about her life: Is she married? She tells him she’s divorced, having made the wrong choices. Stevens asks her if she ever thinks there is an alternate version of her who made different choices. He gets her thinking and asks that she let him in for one last shot. It’s only 8 minutes. Goodwin agrees and tells him that at the end of the 8 minutes, his life support will be turned off - with Rutledge’s support or without.

Stevens is on the train for the final time. He prevents the woman from spilling her drink and tells Christina that she’d be so much better without Bryan and that they should grab coffee as soon as he is done “saving the world.” He asks her to wait for him and she agrees. Stevens races into the bathroom and deactivates the first phone. He looks for a second one and finds it on the other side of the bomb. He pulls the wire out, diffusing it successfully. He then walks up to the conductor and bumps into him, lifting the handcuffs off of him in the process. He goes straight for Derek Frost as Derek leaves his seat and pulls Derek’s hidden gun out of Derek’s pocket. He cuffs Derek to railing and takes Derek’s phone, calling the police and informing them of the plot, calling Derek a crazy piece of shit. He leaves him cuffed to the train.

Goodwin congratulates Rutledge on the success of the program. Rutledge tells her that they should wipe Stevens’ memory and keep him on ice until they need him again. Goodwin is horrified and asks about the deal they made. Rutledge tells her that Stevens may be the only viable candidate they have for Source Code and tells her to go celebrate. She complies but goes straight for Stevens’ body in the container. Rutledge is informed of Goodwin’s transgression and sends the military police after her.

He takes Derek’s phone and sends a text to Goodwin to let her know they succeeded. He calls his father and pretends to be a member of his unit in order to let his father know that he loved him very much. At peace, he knows he will only have 40 seconds with Christina. After giving a comedian 127 dollars to make everyone on the compartment laugh, Stevens asks her what she would do if she had less than a minute to live. She tells him she’d make every second count. He tells her he’d kiss her again and kisses her as time slows down capturing the compartment in a scene of joy.

Goodwin has unplugged Stevens’ life support and looks down at his corpse, which is missing everything below the waist and has wires and electrodes implanted in the brain. MPs break in as Rutledge screams at Goodwin to be arrested but they don’t follow through with it when they see Stevens’ corpse, disturbed at what they see being done to an American hero.

The frozen kiss between Stevens and Christina unfreezes. Stevens is surprised to see that he’s there past 8 minutes and realizes that he has effectively taken over Sean Fentress’ body. He and Christina get off at the next stop and begin walking around Chicago square, reaching a reflective monument. He pulls her close and the two walk off together. He realizes that he is in an entirely new timeline because of the changed events and smiles at having a second chance at life.

At the military base in the new timeline, Goodwin receives the text and reads the memory lines she programmed into Stevens. She is shocked and reads on to discover that they create new timelines when they activate Source Code. He tells her that one day, she’ll be forced to activate him and on that day she will need to help him. The scene ends with Goodwin looking over the body of the new timeline’s Colter Stevens awaiting activation for the next catastrophe.

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