I can see this idea being the basis for the eventual 'Ship Lords' DLC. Refugees start off in civilian ships (an actual fleet on the map), fleeing a war, no weapons, minimal defenses. They enter another empire's territory and that empire is given the choice of accepting the refugees or turning them away. If the refugee fleet is turned away they will have two choices, accept the empire's refusal or deny it and attempt to settle a planet (either adding to the population of an uninhabited world, or colonizing a new world), at this point regardless of their choice any formal empire in whose territory the fleet is in can elect to attack the refugee fleet to attempt to prevent them from settling.
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I would like to see it such that the civilian fleet is created with the same status as the neutral wandering monsters that travel around as they like, with each pop that flees being represented by a single 'refugee fleet' unit which just graphically appears to be many ships and where two or more 'fleets' in the same system will merge to create progressively larger refugee fleets so long as there are none of the 'enemy' in the system.
The creation of these refugee fleet units should be tied to war weariness, with nomadic species requiring less war weariness, and sedentary ones requiring more. Additionally, a planet that has been bombarded by the enemy fleet acquires a modifier for each type of bombardment which reduces the war weariness required to trigger a move. A nomadic species facing a very aggressive 'full bombardment' enemy should find that if they don't resolve the war fairly quickly that their front-line worlds start depopulating pretty quick (though they should also have an easier time filling them back up again later if they're successful).
All empires would have a new policy area for refugees: Allow Freely/Case-by-Case/Deny.
The refugee fleets will move away from the war zone, first dropping units back as pop's onto your worlds if they have any space, or if they're full just keeping on pushing forwards until they enter alien space.
- If the aliens have their Policy set to "Deny" then the fleet just keeps moving through their space harmlessly. It can be attacked by the empire just like space amoeba etc but that should be tied to the policy on purging and should come with the same penalty.
- If the aliens have their Policy set to "Allow" then they should start filling up space on the alien worlds if the habitability is 60% or greater, or otherwise they should start founding colonies on appropriate worlds (i.e. the Blorg wouldn't go join the space penguins worlds, they'd seek out a tropical planet in space penguin territory, or failing that keep on moving through). These colonies are automatically apart of the empire they're founded in, generating diversity for the empire accepting them.
- If the aliens have their Policy set to "Case-by-Case" then they would get an event for each new refugee fleet with the options for "Pick a New World"/"Join Us!"/"Deny" that would generate the behaviour appropriate.
I think this would be a fairly realistic feature that doesn't require heavy investment in new features, as it mostly revamps existing mechanics.