I think there should be several interactions with aliens throughout the game.
Pre-modern: Aliens should very rarely visit your planet either causing damage to structures or abducted your nuggets/taking some resources from planet. There should also be a very very small chance of a crash that allows your nuggets to observe the crash giving a research boost/or a free tech.
Modern: Same stuff as earlier except now you have some ability to observe their species with the tech you already will have to observe space. Also you can now do some fighting back against those visitors with the military.
Space: At this point I would assume they would act like an exile village with some being friendly and other hostile. Since you have spacecraft I would assume their will also be some fleet battles over planets.