So instead of just having the "Space Aliens" (or Zetas as I have been renaming them for my game.) be a typical monster source and randomly abducting people or zapping them with their ray guns, I thought, why not have them manipulate humanity.
A Space Alien advises a council of green men in a remote arcology.
Perhaps have them control individual group types or mix group tribes together in an arcology.
Maybe they convince the humans that there is a plague and they offer them food, shelter and education. They keep them in contained environment and run social tests to see how they can be manipulated or useful. This gives plenty of options for characters to start with some familiarity with the Aliens but are now on the run because they know the truth, or the arcology had an age termination and they are doing the Logan's Run.
Or maybe they indirectly control them by keeping them in Vaults, like in Fallout. The Aliens use their robots and computers to directly train the humans who have lived generations underground. Some of the PCs might escape from a malfunctioning Vault or believed there was no threat outside... (poor character should have stayed put.)