This is not the first success of the Source Code projectFridge Brilliance: Colter actually keeps preventing terrorist attacks and creating new universes where the project was never used. One day the Colter in the new universe made at the end of the movie will be asked to stop another, different terrorist attack and will wind up dead in that universe, having taken over the body of someone in another new universe.
Colter and Christina are going to go to India.Christina mentions wanting to go there, and if they decide to engage in spiritual reflection with some gurus, Colter can act differently than Sean would, do to "finding himself."
Colter died, and went to heaven.Or Hell. Or something else. Take your pick, but he most certainly is dead.
There are multiple Colters in the worldThis was just the first one who was either willing or able to get in contact someone at the base.
Colter can only exist in one place at once.Or rather, his mind can on exist in one place at once. When he's send into Source Code, his mind exists there. Once the 8 minutes are up, his mind returns to the "real world", until he's send back again. Once his life support is cut off in the "real world", his mind can only exist in the source code, so he stays, causing a new timeline.
Colter never even joined the Army.He just started getting really high while he and his friends watched Black Hawk Down. When the film finished, they were a little less high than he was, so they while they watched The Matrix, he started to imagine being an actual Army helicopter pilot. He begins to imagine that he has crashed and woken up in a box full of computers and then that he's a dead guy in an alternate reality machine. The end of his hallucinations meld into a daydream about hooking up with the female friend he has a crush on by taking over the body of her boyfriend.
The director has no idea what he's talking about and did not invent the components of Source Code, he just worked a misunderstood mental other-universe targeting system thingy into a past simulation.Designing such a thing, then thinking it does something totally different and having kind of silly Techno Babble to explain it, doesn't seem like the thing the machine's creator would do, even after discounting the Techno Babble from a Doylist perspective. I find it likely that Rutledge was given a Lies to Children style speech from an associate of his who worked in quantum physics and/or bionics, built the thing, then added a bunch of other components to turn it from a What-If Machine into a Mental Time Travel mystery-solving device that the military and patent office considered unique work (assuming he didn't steal it outright).
The ending is in Colter's head.The source code program is based on using the brain energies of a recently dead person for eight minutes, right? When Colter's life support gets terminated, his brain is still firing for eight minutes, imagining up the end where he and Christina keep living and he makes a difference in the real world. That is why it goes against how the program is supposed to work, because none of it is real.