So if I'm reading this correctly, in your thought this was a big Mount Weather for the High Lords of Terra and the Senatorum Imperialis. That well went "Rogue".
In the USA after Sept 11, for the 1st time officially the Continuity of Operations plan was put in play involved a rotating staff of 75 to 150 senior officials and other government workers from every federal executive department and other parts of the executive branch in two secure bunkers. Prior to that and post that a # of exercises to test continuity plans have been done.
Now given the "oddities" of Warp and Commuication, I can see how the someone could have hit the switch that said, nope not a drill, you are the functional command, and well by time someone figured out that it was a "Mistake" how shall I say Power Corrupts, we aren't giving this up without a fight.
Mission Ideas, bringing neutral planets under their protection. deal with a group of "pirates" (In truth, part of the Imperial Fleet who refused to answer the call of either Terra or Nova Terra, a more DH style game idea (deal with "Heretics" who try to overthrow the Nova Terra system