
Control Center
This is where all the computers are. You'll find the mission computer, used for accessing the Silver Mantis Strike Force, and an aspect of the Pillar of Ice and Flame, used for flashing back to old story arcs.
Transportation
Here you'll find teleporters to all of the available zones, the low level ones are near the door, the higher level ones at the back.
Equpiment
This area contains many bins for storing inspirations, salvage and enhancements, as well as an invention crafting table. Take what you need, and leave what you don't. (Please leave the Embrace of the Earth inspirations for Hami raids though.)
Entrance
This is the place where you normally arrive at the base.
Medical
This is where you arrive if you choose the "Go To Base" option while defeated. You'll find a machines here to dispense small inspirations, as well as another inspiration container.
Conference Chamber
This is the room where all the big decisions are made. It's open for parties too.
And Many more
There are plenty more things for the curious villain to discover. But be careful, you wouldn't want to be caught in the dungeon alone.