* The capsule Colter finds himself in after coming out of the Source Code and communicates with Goodwin in is [[spoiler: a manifestation of his unconscious mind sensing the life support box his body is being kept in, which is why it expanded when he became aware that he was all but dead.]]
** If Colter [[spoiler: survives Goodwin taking him off life support]], because Source Code [[spoiler: works by actually transporting the operative into another reality]], what about all the [[spoiler: realities]] of all of Colter's previous attempts? Is there a [[spoiler: new reality out]] there where [[spoiler: Colter beat up that Indian gentleman and then Christina witnessed him (Colter/Sean) get run over by a train?]] Or, because Colter [[spoiler: didn't stay in them]], do they not exist anymore?
*** [[spoiler: Also comes with the Fridge something, when you realize that the ability to affect/create a new timeline means that as far as the pre-Code version of Colter, his 'first' Source Code mission never actually occurs while at the same time, his conscious (from each post-first mission) slowly spreads from person to person that he jumps into. So from the perspective of his body, he never gets taken off life support since he's always being prepped for his first mission while from the perspective of his multiplying conscious, there's more and more of him out there.]]
** [[spoiler: What happens to Sean in the ending, anyway? Did he just stop existing because he happened to be similar enough to Colter for Colter to [[GrandTheftMe hijack his body]]?]]
*** [[spoiler: Colter appears to be absolutely fine residing in Sean's body without letting anybody else know. The woman who had already fallen for Sean (having waited, for months, for him to ask her to have coffee) has no idea that he's been [[BodySnatcher body-snatched]] by a soldier from a parallel universe; his parents will never know what happened to their son; his friends will never know why he [[NotHimself suddenly dropped all contact with them]], and his students, at least some of whom he's probably formed close, mentoring relationships with, will have no idea that this is a different man. Sure, he might be "close enough" to Sean psychologically to be a good fit, but just imagine any of that happening to your loved one, your child, your friend, or one of your favorite teachers. Or to you. And when he sees his reflection at the end of the movie, reminding himself of all of this? He's smiling because he's next to the woman who will never know she's with a different man. Brrr.]]
** [[spoiler:Once Colter successfully saves the entire train from being blown up and goes on to live with Christina, it shows Goodwin receiving his text message and looking in on Dr. Rutledge, who is now waiting for a new crisis on which to test the Source Code, with Colter still kept in a stasis. Assuming the project is not terminated at some point in the future, how many alternate futures could be created where an alternate Colter has taken over the mind of somebody, like whole root systems growing down away from a central tree?]]
*** [[spoiler: It rather depends on how the Source Code "create-a-new-world" thing works. Since this new world exists soley because of the Source Code there's a good chance Sean Fentress never existed there except as Colter. He's still going to have the personal relationship issues mentioned above, but he's not body-jacking anyone.]]
** [[spoiler:The happy ending is all well and good, until you realize that Colter still has no memory of Sean's life beyond the eight minutes he repeatedly spent on the train. If Colter gets to continue in the alternate reality as Sean and pick up where Sean left off, he's going to have a hard time piecing together all the details he's supposed to know without looking crazy. He had a hard enough time getting down his encounter with Christina, and this time there's no [[ResetButton Reset Button]] to undo his mistakes]]. All he really has is that one perfect freeze-frame moment on the train.
*** To be fair, it seems like Christina apparently prefers Colter to Sean, so he should be alright (at least by Hollywood standards).
*** Also, it's shown in montage that he goes back over and over again before he finds the bomber. Perhaps some of that time was spent, say, going through his bag to find out more details about himself.
*** Never mind that Colter's going to have to spend the rest of his life as a teacher a career he might not enjoy.
*** I'm pretty sure people are allowed to change jobs. If Sean had a decent savings nest egg, Colter can retrain as something else he'd rather do for a living.
* The Chicago police are going to be looking for that guy who handcuffed the bomber, and made the 911 call. His fingerprints are on the phone, and a lot of the other regulars on the train know more or less who he is.
** On the other hand, it's possible they never get enough info to go off of. No one seemed to pay much attention to him following [[spoiler:Derek]] on the train, so exactly how much reliable eyewitness testimony can be found is debatable. And while they have his fingerprints, it wouldn't do them much good if they don't have definite samples from him.
*** Not to mention that even if they have the best fingerprints in the history of fingerprints, they'll only have access to criminal records fingerprint database, so, unless Sean has been arrested for something, they'll never get to him and will probably drop it after some time.
* The text message that Colter sends to Goodwin is not identical to the one that Goodwin receives from Colter.
* At the end of the film, Colter Stevens [[spoiler: saves the people on the train, gets the girl]], and finally achieves some closure in his life... until you realize [[spoiler: he has permanently overwritten the mind of another man and is now living a stolen life.]]
** Except, [[spoiler:the man is dead in our universe. He is only alive as Colter in the pocket universe because of the project]].
*** Here's where the FridgeHorror sets in: [[spoiler: The pocket universe was a ''theory,'' which Rutledge gets wrong at least once. By the end of the film, Colter actually succeeds in changing the past because Dr. Rutledge and Goodwin have never heard of the accident. Why? Because Colter stopped it. Colter jumped into a dead man's memories, changed the past, and has decided to chill there for the rest of his life.]]
*** Actually, the final scene with Rutledge and Goodwin appears to take place in the new universe. The real FridgeHorror hits when you ask yourself: did Source Code really CREATE these new universes, or were there already an infinite number of universes identical to ours?
* I found this quite tricky to follow, but work with me here: [[spoiler:So he goes back in time and in one life decides to call his dad to say "I worked with your son, he was a great man etc. etc". If we assume that an attack like the train bombinb happens once a year, that means that, with Colter not remembering any of his past lives, he will continue to call his dad every time, meaning that his dad will never be able to forget him]]
** It's possible that those timelines don't "overlap" like that, but it's hard to say.
** It would happen in a different reality each time, because every trip into the Source Code is a different reality. It's the same reason the Rutlege we see for most of the film didn't [[spoiler:receive the phone call]].
* [[spoiler: In every alternate Universe (including the one depicted as the ostensibly happy ending) Sean Fentress dies and Colter steals his girlfriend. Not only this, but she doesn't even realise that Sean has been replaced with an impostor. And Colter seems completely fine with this. ]]
** Think that's bad? [[spoiler:Think about this: EVERY timeline that Colter failed except the last two, the Dirty Bomb was detonated and MILLIONS died throughout Chicago.]]
*** [[spoiler: Not quite. the dirty bomb has been detonated in any universe because in every universe that Colter goes back into he travels to before the bomb is detonated.]]
*** [[spoiler: I think the point is that every universe continues after the end of the simulation, since that's what happened with the last one. In which case, there were several dirty bombs detonated after the end of every simulation. We're basically sacrificing alternate universes that we create to save our own. ]]
*** [[spoiler: Though it may be that alternate universes can only come into existence with a mind to create them so they only "real" alternate was the last one because the others never had a permanent reality and [[Film/AustinPowers oh no, I've gone cross-eyed]]..]]
*** [[spoiler: I think there is only one alternate universe. The same program is being run each time, so logically the place and time Colter goes back to is always the same one. Each time he goes back he is reliving the same 8 minutes in the same universe: not the same 8 minutes in a new universe each time. This means that only the final run-through is going to be the defining one. When you look at it like that: in the original universe they got info about the big attack and stopped it, so the only casualties were the people on the train. And in the second universe, there are no deaths at all, and Colter-Sean tells Goodwin that the source code worked. Yes, Colter takes over Sean's mind, but he was going to die anyway in the train. He's going to have a lot of explaining to do, but ultimately both universes are better off after Colter's help. I still think the film should have ended with the perfect moment though.]]
*** [[spoiler: Actually, the real number of dirty bombs detonated is aproximately ZERO. In all the timelines that Colter(The SEAN of that timeline) failed to prevent the train bomb, the source code program was used (It is explicitly shown that the only reason for not using it was that the train was saved), and we can assume that the Colter of those timelines succeded in identifying the bomber and stoping the dirty bombs, the passengers of the train did die in all those timelines, tough ]]
** Also, [[spoiler: Colter has no idea who Sean even is. He knows his name, possible occupation, and picture from an ID card, but Sean could easily be married (it's implied that Sean and Colleen didn't really know each other that well). Not to mention helicopter piloting doesn't exactly transition well into teaching leaving one to assume that Colter got fired soon after the events of the film.]]
*** [[spoiler: And of course he has none of Sean's memories or experiences, so how long will it be until Christina (among others) realizes it's an impostor? From her point of view, some random guy erased her friend from existence, stole his body, and used it to seduce her.]]
** A bit of further FridgeHorror: [[spoiler: Imagine all the people in the world who experience [[http://en.wikipedia.org/wiki/Capgras_delusion Capgras Syndrome]]. Now imagine that all those people are ''right''.]]
*** And it goes on: [[spoiler: If, in future, Colter is ''always'' successful at preventing atrocities before they happen, then Dr Rutledge will never know that he's actually used Source Code, and presumably the government will get fed up with funding a project that never gets used. What happens to Colter then? It's implied that he's the only human subject they have, but what if there are others by then who don't want their life-support turned off?]]
*** [[spoiler: If they're always using Colter as their quantum leap-informer, they will notice at one point that all the strangely averted terror attacks were foiled by someone using the same M.O. over and over again. Which should give them a hint that something ist really really strange.]]
*** [[spoiler: Actually the source code is not a time machine. He saves someone in an earlier run, but she is still dead when he goes back to the original world. The source code is an alternate universe: Colter brings back the foreknowledge of the attack to the original world so they would know that source code was working.]]
*** [[spoiler: That it true for the original world, but in the alternate universe's the source code may never be needed. if Colter has perfect runs in ever mission then there could be a universe where the Source code is never used.]]
*** [[spoiler: In that case, it'll probably be conspicious that all major terrorist attacks in the vicinity of the city are thwarted with some weird fall-guy chained to a railing who admitted to the crime via voice-mail. After all, who says Colter doesn't have the same M.O. all the time he saves the day?]]
* [[spoiler: If the movie follows the Many-world interpretation of Quantum Mechanics, then no reality is being "created" every time Colter is put on the Source Code, but he is traveling into a reality that was already there, and identical (other than lagging behind in time) to the one he comes from, up to 8 minutes before the explosion. This means, that there's a reality out there, in where terrorist attacks never happen again, as Colters from different timelines come to stop each of them, and then parasite the victim on the attack that is closer to them. Which means the Colters and the lives stolen accumulate as time passes, and "copies" of alternate realities going into that time have more and more Colters in them. Those timelines are still better than the ones in where millions die in each terrorist attack, I guess, but the implicaitions are still horrific. Who is going to be the next person that will be unable to be saved just because it's the one closer to Colter?]]
* If Colter is experiencing Sean's memories and experiences, and only Sean's, then how could he have found the bomb to begin with? After all, Sean never knew about it. It was never part of his experience. So how could the bomb have made it into the simulation?
** [[spoiler: It's made quite explicit that source code runs at a quantum level, and an inadvertent side-effect is that the universes it creates are not temporary. As each universe is a carbon copy of the original save Colter's presence in Sean's body, he is essentially exploring the full past and not just Sean's subjective memories.]]
* In the original timeline Colter is dead and gone, rather than sticking around to help avoid future crises, and we've no idea if anyone can replace him. Could you argue he abandoned his own reality and everyone in it for the sake of creating a personal happy ending reality of his own?
* Noticed Goodwin behaves strangely distant at the beginning of the movie, as if she had some information no one else had, and very ambivalent about the whole thing, though readily helpful towards Colter as the movie progresses? [[spoiler:That's because she probably already received a call or text in this universe from another successfully catastrophe-preventing, universe-jumping Colter prior to the events of the movie, who informed her about the potential of the project and asked her to cooperate with this universe's version of him - like he does at the end with the Goodwin from the pocket universe/AlternateUniverse. At the beginning, she still is somewhat confused about this, but the longer the movie progresses, the more she accepts that she wasn't the victim of some very strange phone prank.]]