The establishing shot shows a building surrounded by other buildings. They go to the "Department of Health and Human Services" building, then go into a tunnel... ...but it leads to a hanger, full of military junk. Um, need some help with this one.
Its a big hollow building with a hangar inside. And if you look on top you'll see it has helipads. See how that works? Wait no, That whole building is the base. On the outside it looks like a beat up shit shack while on the inside its a military base.
The Department of Health and Human Services building is a cover for the NEST base. Instead of naming it The Building In The Middle of Washington Where We Keep Aliens And Cool Military Junk So Why Don't You Come Over And Stare At Our Sensitive Intel Stuff they hid it in a place that normally wouldn't arouse suspicion if you just glanced at it like a hundred other buildings in any given city.