I am not sure when or how this happened - there were three factions, and then after destroying one of them, the third faction appears to have become one of the old existing factions.
I can upload the log or save if you wish. I think the result was legit, just confusing. This might have been a rebellion on the last planet of the shadows, which turned into legion who had already been removed from game.
http://www.soldak.com/forums/attachm...d=135811985 9
http://www.soldak.com/forums/attachm...d=135811988 1