it was mentioned its hidden in the game... space ponies was also referenced, and it made me think... the achievement for space ponies is simply "um...what?"
so thats the clue...must be. the eternal enemy is space ponies. the reason the vasari are running is because the ponies are all glittery and sparkly....frightening things really.
seriously though, if anyone read the Clone series of books by Steven L Kent... those aliens are powerful and enough to cause anyone to run screaming for the hills...until killed, as they would make the planet over and deplete the sun, could fit with the whole "darkness comes" theme. perhaps the vasari found a version of these...in pony form?
to slow these aliens down, they used their knowledge of phasic space and nanites to trap them in an attempt to flee, using the dark fleet to periodically re trap the aliens until they again break free.