The government doesn't deny it. They have daily tours with interactive exhibits like "Hangar 17," where tourists can help rivet panels on the new Singularity-powered Troop Transport nicknamed the "Dan Cooper." It's a crowd favorite.
As for what's under it, in order; some rock, harder rock, hot rock, hell, and eventually Asia, where the trans-continental tunnel exits and lands trained troops and crates of Wheaties to China.
Area 51 is soo 1995.
The latest secret facilities are beneath WalMart, brah!