The alien races have one single underground facility on Earth that is for storage of emergency supplies.
The aliens don't stay there, but they hold some meetings there.
The US government knows it is there, and so they built around it to claim it is their own.
All other underground bases are strictly human military.
The leading governments have many underground bases.
No alien races work in human military bases.
The alien races do not work directly with any governments.
Supplies stored at the alien underground facility are food and medicine.
The governments are doing lots of secret things underground, but I don't know what they are or what they are for.
I can imagine what, just like you can.
My alien contacts would not give me information about what the governments are doing in secret.