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No idea why people think the ended was bad, without the bits about alternate universe and her finding out just how powerful the machine was, they discussed it throughout the film to a degree, what the machine could/couldn't do and without the end bits that would have gone unanswered.
The film is about a machine, and investigation and doing some weird crap, the fact they used that to find and stop a bomber is kind of the secondary story, finishing with stopping the dirty bomb going off is only PART of the story, the real story is the guy, wanting to live, and the technology and not knowing how powerful it is.
I really can't believe so many wanted two of the three main stories unfinished, with the three main stories being, the bomb/train, the technology, him wanting to die/her not wanting to use him as a machine.
Good film, I enjoyed it, I really liked how his situation changed quite quickly, not knowing what was going on, thinking its a simulation and acting very differently on the train, him realising he died and hoping he could change the outcome, and him saving a load of people albeit in an alternate reality.
Essentially assuming the situation was real the way he reacted from one simulation to another as he worked out various other things felt, very real, the confusion first time, the no idea what was going on, then treating it like a sim and being completely different, treating the people like they aren't real, then starting to like the woman and realise these people had really died, etc, etc.