I was reading this and got really sad. Imagine being an alien species that is just discovering the universe, just to find out every other civilization is dead and the universe is about to end. Imagine the loneliness.
How about having a simplified simulation of the galaxy while the players species is bound to their planet. Like having species and planets but not fully generated,so they would just be names and some traits,and having them generate when the player enters the space stage or before they interact with the player.
Yeah, that's true, you're not supposed to dodge censors, so GRODOG please don't do that anymore.
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I like the idea of an alien invasion. Goes with the idea of special events that will make each game play unique.
Another special event could be that intelligent life has already evolved on your planet. this could be a good or a bad thing depending on your evolution. for example if you are a big, gentle hunk of meat like a cow they might want to farm you. If you are more like a dog then you could become a pet or go to war with them. if you are something like an insect them would dislike you and try to exterminate. they might also try to collect and study you (just like we do).
The special events could build on themselves. for example the pre-existing inteligent species could get invaded by an alien invasion. affecting you and possibly leading to a change in your species role/evolution (freeing you from the previous species or allowing you to surpass them). I think that special events like these should have a randomized chance of occurring each game although you may be able disable or enable them to make sure they will or will not happen.