Look at the Vasari tech effects in a late game--they have incredible power and that's their "mobile forces" on the run. In the day, their empire must have been epic.
Now look at the primary areas where they focus tech:
- Gravity/Phase Manipulation
- Genetic Modification/Augumentation
- Highly Developed Multiple Purpose Nanites
Then you look at the game title and premise, "Sins". So the question is, "What is the sin of the Vasari that unleashed such judgment on them and who did they sin against and what enemy has it brought to them?".
If their technological power caused their dilemma, I think the gravitic/phase specialization points to a real possibility of a breach in their universe to "something else". Maybe they opened a hellgate , summoned Cthulhu or transgressed into the domain of godlike beings or perhaps it is something they did to themselves...think of what a Vasari "Umbrella Corp" could do. Maybe Milla is after them It could be they opened a portal to another universe or dimension adjacent to phase space or on the other side of a wormhole, modified themselves augmented with nanites to survive there and tried to expand their conquest there--only then to find things weren't simply a matter of mere arms and force and that they didn't just go in but let something out that they can't put back.
But I personally don't think its simply that they found as technologically more advanced race and are fleeing it. I think it is something that absolutely terrifies them for their very existence.
The one thing that could do that for sure would be something that can twist the very nature of reality and turn their universe into a living hell.
If you saw in the last Battlestar Galactica series, when it was revealed that "god" was behind human and cylon creation, the more atheistic cylon simply couldn't deal on that level and then blew his brains out.
I think the Vasari did not find another race simply "more technologically advanced" than themselves--I think they found one so fundamentally different and alien and powerful that it shook their confidence and reality.
So it has to be space ponies.
But in defense of Event Horizon--how would you react if not only did a ship come back after 50 years and the recovery crew went mad but then you discovered the original crew was still alive and would never die suffering horrible torment and the thing that had them was now going to rule your universe too.