First just to get this out of the way I loved the movie. Just on an entertainment level I was engaged the entire time didn't get bored, and the timing of the movie was great. I felt like everything flowed well, and although the ending left me with a weirdly empty feeling I think it was meant to be that way.
This movie will make you think, that's the purpose of a great movie to promote thought amongst its viewers. It does not wrap everything up in a neat package to be easily digested. If your looking for something simple with easily explained plot points and a clear meaning in the end, you're watching the wrong movie. Everything doesn't always make perfect sense, such is true in life and it is also true in this movie.
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The people who said the movie had too many plot holes, I don't think you were paying attention to the movie. The main "plot hole" I keep seeing (even from pro reviews) is, where did the Tethered come from? Red clearly states they're a failed government experiment, abandon when the gov't realized you can recreate the body but not the soul. Clear origin story right there. That's the one that bothers me the most, the other "plot holes" are objective to your own interpretation of the movie.
The larger message or meaning I got from the movie was, the difference between a normal upstanding productive member of society as we know it, and a monster with only primal thought and ambition is merely the environment in which they are placed.
Finally, I love the fact that I left the movie wondering who was really the villain, was there actually a villain? Are we all just victims of circumstance? Do we actively control our own destinies? I think the movie did a wonderful job of making you think about which side of "Us vs Them" you are really on? Everybody always thinks they are a part of the "Us" but maybe, just maybe...You're a "Them"
Great watch, with an open ending that allows you to debate it with your friends the next day.