Just a crazy idea, but has anybody considered a time travel plug-in? Could be your character is some kind of time traveling security force agent, sent to carry out various missions to prevent tampering with the timeline. I imagine you could do it in the regular Nova universe, based on what we know of the events in the past in that universe. Maybe some crazy Rebel scientist is trying to destroy the Federation so it never becomes a major power, or some Auroran minor house is trying to become a great house by altering the events leading to the stable relative unity that the Aurorans now have?
I imagine the time travel part wouldn't be too hard, you'd just need multiple copies of various parts of the universe. You might not have to alter all that many systems, just restrict the player to operational areas, use some kind of ncb to control what shows up on the map, and give a few simple enough missions, mostly combat, some escort perhaps, and a compelling story based in part on the various story documents ATMOS released.
It's no TC, unless you really wanted to create a new universe, and it could be pretty neat.