I have NO idea about 9/11 as I had already left the service 3 years before but I'll share with everyone here what secrets I DID learn of when I was in the military...
ALL this stuff is from people way higher up than myself, including a Brigadier General I was personal friends with!!!
1) JFK got himself in BIG trouble not supporting the "Bay of Pigs" invasion of Cuba once it was started, when asked he said NO to airstrikes to assist the invasion and the CIA went against him.
P.S. As a side note, he DID have many mistresses and the CIA was tired of following him everywhere!
2) There does exist a NUCLEAR powered plane, it flies from Nevada to an airforce base in UK in 20 minutes- only thing I heard it's called "Dark Star". Because of the fact it puts raw radiation out in the atmosphere they don't use it much anymore (after 1998).
3) I did hear the Moon landings were all filmed in the area around Area 51, directed/filmed by the great Stanley Kubrick (who did 2001: A space Odyssey).
That's about all I heard, I know it's dated, etc... but it was hot at the time!!