Quoting Rhonin_the_wizard,
I had a similar issue. The Drengin destroyed one of my shipyards and the whole universe stopped in shock and horror, never to move again. Needless to say I never allowed that to happen again
Not much we can do without a savegame.
Yes, I know. Too late now. To be fair, it has only ever happened once. I have a LOT of issues with IV but it is very stable in my experience which is a big plus point.
I also ought to give you guys credit where it's due: I was at the point of giving up on a game because I was obviously winning but there was so much work to do to eradicate the remaining aliens when up pops this "Prestige" Victory. wtf? I didn't know it existed but it's a brilliant idea. Does the AI actually compute that you will inevitably win and give you a quick victory?
If so that is one of the best additions to any game I have ever played (Civ 6 please take note)