I wonder how to explain/handle the spaceships
Maybe they spread on pirate/rebel/refuge ships, either by hiding out or by entirely taking over?
How to make them not to aggressive vs the player? Note: I made them partially self contained in terms of territory (for example The Hive have 3 overminds on various planets and they can/want to colonize only up to 3-5 jumps from the overmind) so it helps to an extend...
But I'm not sure I want all of these local aliens contained this way.
Maybe they're in smaller clusters controlled by these overminds, but after a certain time a larger overmind unites them all and causes them to agressively expand? If the player kills this overmind the expansion stops -- maybe those further from the smaller overminds even lose morale or become disorganised and can be easily removed, until a larger overmind grows again.