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Are we sure the Pentagon was that group of hijackers' first choice? Maybe they wanted to hit the White House or the Capitol, but realized they couldn't do it and made a last-second decision to hit the Pentagon instead. (If they REALLY wanted to hit the Pentagon, and if they really had the training to do so, why didn't they aim for the part that contained the SecDef's office? Surely the Evil Geniuses at Langley would have known what part of the building to hit.)
If the planes were piloted by experts trained by the CIA or whoever, then how do you explain the crash in nowheresville, PA? Wait, lemme guess...the Evil Geniuses staged it to LOOK like a failure, to disguise the true scope of their Evil Genius...
See how easily "conspiracy + coverup" can be made to explain ANYTHING? And in the sciences, it is a basic principle that a "theory" that can explain anything, really explains nothing.