One of the important questions about September 11th 2001 is why the response of the air force was so ineffectual. There has been widespread speculation that there was a blanket "stand-down" order of some kind, but that never seemed at all plausible.

One of the things that Mike Ruppert discovered and documented in his book "Crossing the Rubicon" is that there was more than one military exercise going on at the time (including a large-scale simulation of a multiple hijacking), which had the effects of removing many fighter planes from the area and of creating massive confusion in the response to the events. Furthermore he has evidence that Dick Cheney was coordinating these exercises.

There is a summary of the argument of that part of the book at:
http://www.fromthewilderness.com/free/ww3/011805_simplify_case.shtml.