Here is something I've been planning and working on a little at a time for the last few months. Its a covert base for my 25th figures. So far this is the basic layout. I got two of the PTE HQs and modified them to stack on top of one another. This will be the above ground portion, moderately disguised as a house or something like that. The below ground section will be made up of the Treehouse Aliens set and some add ons I have yet to get. Possibly some Joe HQ components like the vehicle bays off to the sides or something.

This is the upper level and rooftop observation deck. The upper level will be barracks and R&R section with some bunks and lockers, a table and chairs and if I can find one a TV set. Someplace where the troops can kick back. The roof will be an observation area and have some small radar and communications antennae. Also sentries will be posted up here for guard duty. There is roof access through the existing hatch and a ladder I'll be getting from Marauder.

The main floor and sublevel 1 are shown here. The main level opens out to "street level" and serves as the main planning and conference area. It has access to the upper floor and sublevels via ladders. The main level has an observation deck that overlooks part of sublevel 1. Sublevel 1 serves as the main armory. The majority of the team's weapons and armament will be stored here.

Sublevel 2 is the motor pool and engineering and maintenance level. Off to one side will be access to the main vehicle bay housing the R.H.I.N.O. The vehicle bay will lead to the surface via a lift that opens on the side of the house. Not completely stealthy but no more obvious than Batman driving the Batmobile into a cave under his house.

Now I'm just wondering a few things. Like I said, I want to use parts from the original Joe HQ to fill out the lower levels. Maybe adding vehicle bays to SL1 and SL2, stacking them in some way. I don't want it to get too wide as I need to fit it on a shelf or small table in some way. Also need some ideas for fleshing it out. Computer consoles, equipment and the like.
As for the floors and walls, the upper levels will get closed in with some foamcore walls and printouts from Joedios. The floors will get a treatment as well. The lower levels will get a new backdrop and floors as well.