Actually it wasn't a missile. It was a projectile from the Navy's rail gun. The part of the Pentagon that was hit housed Nazi gold from WWII. The Rothschilds were keeping it there because The Pentagon is sort of like Gringotts form Harry Potter. All the valuable shit is stored above ground at a building that can be hit by projectiles. But that's the genius of it. It's the last place anyone would expect for critical communications systems to be or lots of secret gold or whatever.
Area 51 isn't the only place the shadow governments keep secrets. A pentagon has 5 sides. Area 51. 51 = 5 and a 1. The pentagon is building 5 of the millennium archives. Area 51 is building 6. 5+1 = 6. The millennium archive is where all our nation's secrets are held.
"Astronomy offers an aesthetic indulgence not duplicated in any other field. This is not an academic or hypothetical attraction and should require no apologies, for the beauty to be found in the skies has been universally appreciated for unrecorded centuries."