Ok. I almost hate to get into this, since I can't even make anyone acknowledge that Rumsfeld deliberately impeded the chain of command that morning, but...
When I was looking through the interviews Rumsfeld made about 911, I saw a very strange statement he made about the debris from the Pentagon attack. He talked about a lot of "tiny" pieces, and how it didn't seem to be from a plane. He says he then spoke with a military officer who told him he'd witnessed a plane crashing into the building, and that's how Rumsfeld says he determined what happened.
A few things I've seen about it, is that it was perhaps a phony flight to begin with, complete with a made-up passenger list, or that it was shot down over the ocean.
As I say, I'd be happy just to begin with the first step of understanding that Rumsfeld made it impossible for the military to be directed that morning. Because once that's determined, it opens up one hell of an interesting path.