(Click for a bigger image.)
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.
Teleportation Nexus
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.
Generator Room
Not much to look at here.
Inspiration Storage
This area contains many bins for storing the various types of inspirations. Take what you need, and leave what you don't. (Please leave the Embrace of the Earth inspirations for Hami raids though.)
Entry Point
This is the place where you normally arrive at the base.
Medical Facility
This is where you arrive if you choose the "Go To Base" option while defeated. You'll find a machine here which dispenses small green and blue inspirations.
Enhancement Storage
Here you'll find many bins filled with a variety of enhancements. These are free for anyone to take. Feel free to drop stuff off here, if you feel it may be useful to someone else.
Research and Development
Here you can find tech crafting tables, used for crafting base items, as well as personal empowerement buffs. Keep going a little further, and you'll find another workshop with arcane versions of the same facilities.
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.
