Sometimes you acquire faction specific prisoners and colonists. I can turn in the prisoners to the security officer, although not much of a reward and not sure why this exists. What do you do with faction specific colonists?
Colonization assignments at the former exploration clusters, a couple of fleet projects and an assignment from the Operations Officer that gives 500 raw dilithium for 5 colonists. The Exploration Clusters are now nebulas on the sector map that only give Duty Officer assignments and Foundry mission entrances. Completing each Exploration Cluster chain gives a unique rare duty officer and a unique very rare duty officer provided that you crit the repeatable assignment. So you can have a bunch of very rare Borg Kitties (Liberated Borg Caitians) for doing the B'Tran Cluster.
#1 - Colonization missions in "exploration cluster". Colonization missions have 7 missions which eventually unlocks a Colonization Expansion / Support mission which rewards a specific very rate Doff on a critical success; this is a repeatable mission. I believe two of those missions requires 4 colonists each.
#2 - There is a mission called "Relocate Colonists" which requires 5 colonists to start. I believe it is a daily mission (20 hour cool down) that rewards 500 Dil. The related missions is called "Resettle Colonists" it requires 3 Doff to start and it always uses your quartermasters first for some reason. It rewards you with 5 colonists and it is available every other day (likely a 40 hour cool down).
#3 - Once all 7 of the colonization missions have been done, the explore cluster should have an "Establish Forward Base" mission or something similar to that phrase and it is a repeatable mission. It requires 3 colonists and rewards 125 Dil.
the fleet project "Coordinate Colonization Efforts" takes 64 of these at a time and/or any extra prisoners you may have,
get your fleet to run it as often as possible
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#2 - There is a mission called "Relocate Colonists" which requires 5 colonists to start. I believe it is a daily mission (20 hour cool down) that rewards 500 Dil. The related missions is called "Resettle Colonists" it requires 3 Doff to start and it always uses your quartermasters first for some reason. It rewards you with 5 colonists and it is available every other day (likely a 40 hour cool down).
#3 - Once all 7 of the colonization missions have been done, the explore cluster should have an "Establish Forward Base" mission or something similar to that phrase and it is a repeatable mission. It requires 3 colonists and rewards 125 Dil.
get your fleet to run it as often as possible