There are loads of potential Deepnight entity prequal scenarios possible. Once you have read The Deepnight boxed adventure you have a better understanding of things that could have transpired in the past.
1 - Death Station, a sample of deepnight entity has been taken to a lab ship, run Death Station but the big bad is now crew and robots possessed by entity.
2 - Archaeological expedition - the usual scientist type thinks they have leads on an extinct alien civilization, after much adventure the punch line is the civilisation was destroyed by entity (or if you want a twist in the tale the civilisation destroyed itself to stop entity)
3 - Chamax plague/ horde repurposed - instead of the insectoids it is entity possessed insectoids...
4 - Interdiction - the Imperium is interdicting a world due to its problems with deepnight entity possession (wouldn't surprise me if the Imperium hadn't scrubbed a few worlds in the past)
Don't overplay the entity though, the players should be left guessing about its true nature until you want to make the revelation...