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I'll start off by saying that I was one of the millions of immediate victims of 9/11 as I was living in New York City and working near ground zero in Lower Manhattan at the time.
I don't think the attacks themselves are in any way connected to any conspiracy by the Bush administration. It would have taken the cooperation of hundreds if not thousands of people and given the amount of destruction, the number of lives lost, and the blatant power grabs and attacks on our civil liberties since, I'm certain someone involved would have come forward and exposed it.
I do however believe the Bush administration was aware hijackings were planned and prepared for a much different scenario than the one that actually played out. They weren't sure of the exact timing but the fact higher level government officials like the Ashcroft stopped taking commercial flights shortly before indicates they knew something was going to happen.
Instead of the hostage scenario they planned on, thousands of people were killed. They couldn't admit what actually happened because it would have been political suicide for a president with already dropping poll numbers, so they made lemondade instead and they've been using it ever since.