Those articles are definitely trying to spin a conspiracy theory when one probably doesn't exist.

First, a few things. NORAD has no direct control over any missile silos, air force units, or other military units. They simply watch and report. Forget Wargames, nothing in that movie beyond NORAD being located in Cheyenne Mountain is true (and even that is not completely true, but moving right along...)

If Bush knew about the first attack at 8:46, he knew probably very little. He probably thought it was an accident. Most people did at that time, and that was the first time in history that a hijacked plane was used as a weapon and not a negotiation tool. It took the second plane and masses of cameras watching for anyone to realize the depth of the problem. Plus, if fighters had been scrambled, they probably were not expecting to shoot down anything, nor were they expecting mass chaos. If the base near the pentagon was staffed well enough to have them up right away, they were probably en route to New York since at that time 2 planes were already around there. Again it's hard to say though from the public standpoint.

I suppose my main point would be up until that morning, no one in the world expected what happened on 9/11. No training had anyone prepared, no one had their thought process aligned properly to deal with the situation. All our leaders do have some extraordinary qualities, but they are human just like us, and work much the same as we do here. For a geek, what would be your first response to a crash under Linux looking like an NT blue screen?