Non-convoluted / literal explanation of this film
Aside from the existential "nature Vs. grace" message of this film, which it does a horrible job to even define or explore, here is exactly what it's about:
Brad Pitt's character was obviously physically and/or psychologically abused by whoever raised him and he is continuing the same cycle with his children.
He wants to be tough on his boys so that they can be tough and not taken advantage of in life.
The youngest of the 3 boys gets abducted and killed by the guy who was the clown at one of their birthday parties. This is the death that is mentioned at the beginning and evidenced by the crying, the phone call, and the glimpses we get later in the film of the creepy guy and the little boy in the attic riding the tricycle and the images of the creepy clown at the birthday party.
The oldest boy is resentful of the father's treatment but realizes it was necessary because, as I said, the youngest is lured away by the stranger and murdered.
I can't believe everyone one of you missed that. They made it all painfully obvious as long as you were watching the whole movie. Go watch it again!
The end of the movie (the watery wasteland seen throughout) is obviously the afterlife, where everyone meets on this neverending shoreline.
That's it. That's the plot. Stop trying to turn it into something it's not.
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My list of 1,100+ wild 'n weird movies: http://www.imdb.com/list/ls053942167/