hate to go off topic but this raises a problem in the game. perharps a check if there is a ship that has colony module, SY or troops would be useful? (those are the things one would requie to survive - any of them)
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I dunno - I kind of like that empires remain in play when they have something that exists. In fact, I'd probably use an option that removed knowledge of when an empire was destroyed, because it is artificial knowledge.
If players see that everyone is at peace, they've explored the whole quadrant so they haven't missed anyone, and they want the game to end, they can end the game voluntarily.
I like the ability to survive with just some ships, even without a SY or colonizer. It gives the chance someone will donate such resources, and also makes some things more possible to survive like monster/pirate/nomad races.
I'd think the crucial determining factor would be population. If all your original population is dead you'll have to enslave someone else's population to survive and grow again. But is that really still the same empire? I'd say not. Maybe there should be some way to recover your race from ships that have crew quarters if all your planet population has been destroyed?