Here's an interesting article I came across about 15 of the world's most infamous top secret sites. There isn't much revealed about any of them, but several do relate to 9/11, from the remains of Flight 93 stored in Iron Mountain to 9/11 suspects at Guantanamo Bay to Site R @ Ravenrock in Pennsylvania which was visited by five helicopters and a convoy of SUVs shortly after the Pentagon was hit.

http://www.otbeach.com/news/security--5/15-infamous-top-secret-bases-&-compounds-from-around-the-world--495.html