I don't know, clearly aeroplanes were used to crash into the World trade centres and one crashed on the ground. Why not crash one into the pentagon too. Why risk a missile? Perhaps the smell of cordite could have been from explosives kept inside the pentagon. I saw a segment on TV that was built around the investigation on how the towers could tumble from planes crashing into it. It looked pretty convincing. Just because they were the first towers to fall due to fire doesn't make its a cover up.
And it begs the question, why would they do this, why kill so many people. I can not see how something so horrible and on such a large scale would be kept secret from being the main cause of the incident because it would need the cooperation of thousands from the FAA to the NYPD and I can't believe those people involved would be so cruel to do such a thing and not feel guilty enough to say something.
And it still doesn't explain what happened to the plain that was meant to crash into the pentagon.

The most I can see out of this is that the CIA or whoever knew about the attack and instead of doing nothing they just helped out. Like backburning during buh fire season. Control the level of damage done. What do you think?