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But I can not for a single second entertain the idea that [Bush] could have set up 9/11.
Why would anyone have to set it up? By the late 1990s, al Qaeda actions were as regular (if not as frequent) as the tide — so much so that Clinton had his national security advisors draw up the plan for invading Afghanistan as the only way to be sure to put an end to them.
All one would have to do is drop the Afghan plan, stop listening to field reports, and shelve a few national intelligence estimates — and the outcome would be foregone.
Let's look at your own (quite valid) point about the "Tower 7" speculation, only in reverse: for it to be an accident that the Bush regime totally failed to stop the inevitable (and, as it turned out, well-predicted) knock on the door by al Qaeda, the number of people all "missing the memo" at the same time would have to be astronomical.
Whether Bush and his regime were criminally negligent or just criminal may be debated — whether it "just happened" may, rationally speaking, not be.