Are you making the Deep Ones humans that were modified. or did a starship full of Deep Ones come across a human colony that they decided to enslave? Are the Deep Ones essentially Lovecraft's--being immortal--or something else?
Spacehip Zero has a background just like I think you might be suggesting
Spaceship Zero - Wikipedia, the free encyclopedia
That game system is a percentile based game heavily based on BRP. The enemies that are enslaving humans are essentially Deep Ones.
http://greenronin.com/designer_spotl...erview=sszchat