Universe A: the train gets blown up. There’s intelligence that a much bigger attack will hit, and the Source Code project is activated to see if they can get any information because people kind of like downtown Chicago when it’s not a radioactive deathzone.
Universe B: first iteration seen. Train gets blown up, Chicago presumably does too later, due to our hero being thoroughly disoriented. Try a little briefing next time, guys!
Universe C, D, etc.: Subsequent unsuccessful iterations as our hero tries to figure things out. Train keeps going boom, and Chicago presumably likewise from no information gained.
Universe…let’s call it P for penultimate. Could have been more, because I read montages before that point as our hero getting sent through repeatedly. Train goes boom, and he learns there’s a backup detonator because of it. He also gets the bomber’s identity, vehicle make and license plate #, etc. Granted, he and love interest end up dying in a parking lot, and Chicago in Universe P still goes boom. Still, mission success!
Back in Universe A, Source Code project is successful. Train has still gone boom, but they apprehend the nuclear terrorist before Chicago can go likewise. Whatshername nobly self-destructs her career by pulling hero’s plug.
Universe Q - our happy ending. Train does not go boom. Chicago does not go boom. Everyone lives happily ever after, except Sean, who has been taken over by a parallel-universe body snatcher.
Seems straightforward enough to me.
There’s some pretty disturbing ethical calculus going on depending on whether use of source code actually technically “creates” entire new parallel universes each time it’s used, because each unsuccessful iteration kills that many millions of people “again.” So if Chicago not going boom in Universe A saves five million people, that’s actually at the cost of, say, fifty million people still going boom later–or rather, quantumly parabolically technobabbly parallelly. (Give or take, depending on how many iterations he went through. I’m not saying we wouldn’t get our hair mussed.) Plus, if he’d failed in Universe Q, that would have been especially selfish.
I didn’t like it as much as Moon, but still liked it a lot.