The plot of the film is that Colter Stevens, played by Gyllenhaal, is sent into the memory or 'brain state' of a victim killed by a recent train explosion. Stevens' mission is to find the bomb, as well as it's owner, in order to help those outside of the simulation find the terrorist who planted it in the real world. The film takes a turn however, when we realize that Stevens is, for all intents and purposes, dead.
The physical construct Stevens sees himself in is manifested only by his mind, as he is only there in consciousness, not in a physical sense. Towards the end of the film, Stevens asks Colleen Goodwin, the woman overseeing the 'Source Code' project, played by Vera Farmiga, to let him go back in one more time, to save everyone on the train, and avert the explosion. He also asks her to terminate his life support after eight minutes, which is when the simulation ends.
After Stevens saves the day, he finally gets his kiss, and the girl, and when she ends his life, time freezes. What happens after this however, is the subject of many viewers debate. Everything resumes, time starts again, and everyone continues going about their business. Reality sets in, but what reality, who's reality?
Some believe that the Colter Stevens' life is terminated, and what the audience is seeing is his 'heaven', which is extremely similar what his mind saw at the end of the last simulation. While this certainly is a possibility, it's not likely, as the film has much proof in favor of a contrary theory. The film's largest secret is that every time the Source Code is used, it creates a new, parallel reality. So ultimately, Stevens now exists in a world completely new and different from the world he previously existed in.
Each time before, the Source Code opened and created a new reality, however they were each brought to a close for our purposes, as his presence was only validated by the train's existence, and when it ceased, he became nonexistent. These other worlds continued on, but we do not see them, as Stevens doesn't exist in them. Stevens saved the train and all the passengers on it, including Sean Fentress, the person who he 'overrode' when he came into the world. In terminating his physical life he also completed the tear between realities, allowing him completely to exist in the new world.
This is largely evidenced by the text he sends to Colleen Goodwin while inside the Source Code. The film cuts to her, in a world that is clearly an alternate reality, where he has averted the crisis. He implores her to terminate the Colter Stevens in her own world, knowing that it creates another world entirely, saying it works even better than expected.
Although it isn't as clear a hint, the film's credits sequence also clues in the audience. When the film's title appear on screen, below it a single line appears, which then diverges and weaves into multiple more, hinting at the idea of parallel realities that drives the film.
Source Code is a film made strong by it's mind puzzling plot, and it is certainly a film that warrant a re-watch after finding out the truth of the film. If you haven't seen the film, I'd still highly recommend it, even after reading this explanation.
