When you think of underground I can think of 2 big ones, and at least one is concerned with UFO's. NORAD is built into a mountain, and John has connected the AirForce to the collection of UFO reporting to NORAD, as well as civilian aircraft reports of UFO sightings. I know that Edwards Air Force base at least, and I'm very sure most every US base as well especially SAC Bomber bases like Wright Patterson, have a maze of underground tunnels and bunkers. Edwards has a system of hatches all over the base to get into in case of nuclear attacks. They are supose to be a network all over the base interconnected. one can only imagine what they have underground. The origional MX missile, now called the Peacekeeper was designed to deploy using an elaborate underground tunnel system in Utah covering hundreds of square miles. They would continually be moving from location to location all underground. We also staged ICBM's in the cold war inside Barn Silohs, so the looked like any other farm or ranch, but inside the Siloh was a missile. We have housed our ICBM's inside underground silohs since the 60's. Vandenburg is probably moslty underground silohs. our biggest underground weapons are our Submarines.
As far as knowing where they might have alien bodies, take your guess/ All we know for sure is the military has a very wide use of underground facilities, and most are in remote and desolate places. Area 51 has to be a maze of underground secret places. The nevada nuclear proving grounds. maybe the biggest and most remote place of all is one nobody thinks about--underground secret places on Guantanamo--the most remote of all.