From the review of Source Code:In the end, at least one nagging question lingers. Every time Goodwin and Rutledge throw the switch and Colter wakes up in Sean’s body, what happens to Sean? It’s a question that can’t necessarily be mooted as easily as you might think.
Yes it can. Colter’s existance is only in bits and bites playing out in the source code or programming which is the eight minutes of memory. Sean is dead but the program or code of his last memories is being interfaced by Colter. Sean doesn’t go anywhere because Colter doesn’t enter him (Colter is not going back in time) he just enters the coding of his memories.
That’s what Rutledge thinks is happening. That’s not what the denouement indicates is really happening. [Spoilers follow.]
In the end it seems that Colter isn’t merely interfacing with memories — he’s actually interacting with alternate realities, with real consequences in each. In the end, Colter winds up saving all the passengers on the train in another reality — and in that reality he remains in Sean’s body, presumably to the end of Sean’s natural days.
That’s not a moral problem for Colter; that Sean would have died anyway, and he saved everyone else on the train. But it’s a narrative problem for the film, because it doesn’t engage the question and seems not to want the audience to think about it.