The machines did that in order to survive. They used the body from people to run after the sky was scorched. It's supposed to be an allegory anyway about our modern dependence on technology and the nature of reality.
Ironically in terms of an allegory of the nature of reality, I much prefer "The Thirteenth Floor" along such story lines. Oh well. Different strokes....
The Thirteenth Floor (1999) - Plot Summary - IMDb
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