I hate to be the bubble popper here but there are no submarines in the desert well at least not in real life.
it is a training facility where they teach everyone how to run the equipment on the submarines. they have
mockups of all the control rooms. there was a pre-existing base at the location so instead of paying exhorbitant rent somewhere else they built in the
desert. Easier to protect all their super secret tech. if they can see you coming a mile away.