It would be like "historical wars", choose the side and play. eg. Dominion wars - The game starts, you select the Federation. You start off with cannon map (I read that sometning like that was planned), have some ships, stations, and your tech level is developed as they were in that era. Your objective - With the Klingons
you must fight the Dominion and their allies(Cardassians
and later the Breen). To gain an advantage you must get the Romulans
to join you. You will have DS9 and the wormhole in the Bajoran sector (somehow it would be crutial to make the Wormhole the only possible way to go from Gamma to the Alpha quadrant). And you must win.