Lots of good discussion here
My two cents goes something like this.
Looking at this from a realistic perspective ie current technology.
I'm sure there are subterranean bases but I seriously doubt there are very many or that they are anywhere near the complexity most people think.
Building tunnels from one to another is a pretty silly idea considering the time and effort it would take to create such tunnels.
Then again if they have advanced tech that we don't know about then of course anything is possible.
One thing I learned while in the USMC [3rd AABn Alpha] is that the Government is very good at hiding things in plain sight and since the general
public has no idea what they are looking at most of the time anyway I don't see where there is any real need for more than a few " secret " bases
let alone tunnels that go from one to another.
The reality is that the military could easily move anything they want over a normal road and people wouldn't even know about it.
Fun to speculate though