Occasionally I get DOFF missions requiring a refugee. Sometimes I have lots, but its easy (if in a Fleet) to accidentally submit refugees to Fleet Holdings that take civilians. And then... long periods go by where I have no refugees. I have no idea what missions give me more refugees.
Then - Ferengi Traders and Faction Specific Colonists - I get crates of these things. On my non Fleet toons there seems to be no way to get rid of them once the Expanse/Nebulae doff mission chains are done. Is there any other purpose to them?
And finally, Faction Specific Prisoners - seem almost entirely useless to Federation characters. There are a few security officers that will take prisoners off my hands but they do 1 at a time and have quite a long cooldown so its all but impossible to unload a significant amount of prisoners. There are no mission chains (on the fed side) that need them, and the security missions don't seem to give any special reward.
So:
1. Where do I get more refugees?
2. Are there any recurring high quality missions for Colonists or Prisoners that are actually worth keeping them for?
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I think it is rare in availability so it'll be some time between it being there and it has a cooldown too. If it is there it is pretty easy to spot as it is the only one of the cluster missions that gives an "item" as reward. It has the "mystery item" symbol as the first thing among the rewards granted, that's the refugee. (You also get another doff from a critical success, which one depends on which star cluster you picked up the mission from.)
When looking around for these remember to check the four clusters in Alpha quadrant too, not just the ones in Beta. I usually find it worth the extra time when I'm flying around looking anyway.
2) Getting rid of colonists is the easiest and possibly most profitable thing you can do in doffing.
Open the doff UI in sector space. Often you'll find a mission named "Resettle colonists to Federation Border". If it isn't there you can undoubtedly find it under the Operations tab in Department Heads, if it¨s not on cooldown that is. You need 5 colonists, 5 provisions and 1 medical provision to start it, run time is 3 hours and nets you 500 dil outside of double dil events.
If you're on PC I'd recommend you keeping your colonists in those boxes for a bit because we have a double dil event coming up in two weeks or so, then it'll net you 750 dil per run.
2b) Prisoners? If you're Fed, space them. Or use them for Fleet projects if you can. There is that doff mission at the security officer where you can turn them in but it really isn't worth the time it takes to click the buttons. Keep maybe ten or so of them around for the endeavor that sometimes pops up "turn in ten prisoners". Though if you have a KDF side toon I wouldn't even do that as it is more quickly completed KDF side, not to mention more profitable too.