"If non-classic (ie, TGN & Voyager) star trek had the borg, DS9 had the dominion and Babylon 5 had the shadows..then who could be the traveller imperium's looming alien threat? the zho? the k'kree?, solomani? Aslan?...or something more ominous just lurking at the edge?" -- Grymlocke.
What are the common features of a "Looming Alien Threat"? Some or all of these seem to fit.
1) It's enigmatic. We don't know exactly
what it is, where it came from, or what its goals are.
2) It's destructive. Life and Liberty as we know them are threatened. Society fragments.
3) It's quietly insidious. You never know where or when it will strike next.
4) It's subtle. One day everything is fine; the next day everything is somehow
different.
5) It's capricious. The rate of events fluctuate wildly. Months could go by without any visible signs, then suddenly all lost time is made up in very short order.
6) It's inescapable. No quarantine or known technology can stop it, and running away from it only delays the inevitable. The longer and farther you run, the more difficult is is to get away.
7) It's virulent. No matter how slowly it propagates, it could eventually spread everywhere.
"The Blight" -- One day, people just start falling over, dead. No detectable pathogen, poison, or trauma can be found. There is no common cause. The person is just
dead.
"Baby no More" -- Anything that can reproduce loses that ability. Microbes, plants, and animals all die out after living out their normal life spans. Even virii become dormant.
"It Came From Within" -- Random people begin to morph into something twisted and hideous. Maybe they go insane. Maybe they don't. Maybe they just die... painfully.
"Night of the Living Dread" -- Random people begin to zombify; lack of initiative, shuffling gate, reduced mental capacity, and no sense of pain. A small percentage turns into berzerk cannibalistic murderers (e.g., the Reavers from Firefly).
"Where Is Everybody?" -- People go away and never return. They've disappeared without a trace. Those left behind don't seem to care, and soon forget that the 'disappeareds' ever existed.
In each of the above scenarios, there remain a few individuals that are unaffected. These people have two main concerns:
1) What the *&^%$#@ just happened?
2) What do we do now?
If a search is made for The Cause, then clues could be everywhere, but not be obvious until a large number of them are brought together.
And just when the characters think they've finally found The Truth, something happens to show that they are wrong,
again. They may never actually find out what the real threat is, but maybe they find out some way to keep it at bay... or not.
Don't forget the red herrings!