
My brother has been playing Abion Prelude for some time now and has set up seven headquarters in his game. Six in one sector (screen shot below) and one in another sector.
This is without any outside of game programs, scripts, mods, hacks, etc. It is all done in the vanilla game with the current 2.0 build of Albion Prelude and bonus pack.
The screen shot is not photo edited in any way and the save game is posted below in case you want to check it all out.
Not only that, but the game is a near perfect game in economy supply and demand. All totally automatic with 235 ships and 829 stations !!!!!! You can see how to setup a huge empire with no blinking stations and all producing. Space is mapped with 1653 Advanced Satellites so you can see it all. Game was started with Argon Peacekeeper and Terran rep was pulled from bottom to 23% Terran Hero of Sol.
Game provided has no Modified Tag !!!!!
Screen shot -> http://dl.dropbox.com/u/54171727/6-PHQ.bmp
Saved game on slot #1 - > http://dl.dropbox.com/u/54171727/X01.sav
Edited 2012-Apr-12:
Good news at last, we finally have a new game (with many more clues) for all to examine. And this time with a bit more challenge for those that like such things.

Download X3 Master Pro's Conundrum here -> http://dl.dropbox.com/u/54171727/X02.sav
This game will allow you to place your own player headquarters (all 7 of them) where you want them. The game is mostly un-finished. No cheats other than an in game exploit (as previously described) was used to make this unique start. The hub mission is not started yet. Only the Argon main plot and the PHQ mission is completed. But there is a new challenge for you. You'll figure it out when you get to playing.
For those that are just treasure hunting the exploit, this game should be much easier to examine because of a much smaller game and time-line.
Have fun !!

Edited 2012-Apr-17:
For people that don't want to go through a difficult challenge of getting 7 player headquarters in X3TC,... My brother offers the following game.
X3TC saved game on Slot #3 -> http://dl.dropbox.com/u/54171727/X03.sav
Game time is 1 day 8 hours with no modified flag for Vanilla X3TC. Headquarters awaits your placement on Orca ships. No tricks this time.
