What would be the impacts of an alien civilization “vassalizing” humanity?

I’m starting to work on an idea I have for a sci-fi setting. Here is a quick primer:

Humanity has created Moon sized ships called arks. After the ships left the solar system, a cataclysm occurred and the ships lost contact with each other and Earth. This was a generation or so ago.

One of these ships is tentatively nicknamed “The Spheres”. At some point during its isolation it was attacked by a kind of alien intelligence. The war was brutal and ended with the humans losing, but the aliens decided to “vassalize” the ship and rule indirectly. The aliens inserted themselves into the humans’ religions and the humans live in a kind of techo-theocratic-feudalism. The aliens keep a permanent presence on the ship via huge robots that activate to suppress rebellions and destroy anything that humans might use to break free. Most recently, rebels have gotten in contact with another ark, the Sintashta, and are asking them for aid.

What might be some ideas of what the ramifications of this situation might have on society and what the aliens might want from the humans? This is all in the very early stages so it could go in a lot of ways, but I want to keep this idea of a post-apocalyptic setting for the ship.

Any help is appreciated.