There is far too little information for a single theory, so I'm just going to list all the common excuses used in fiction.
For starters - you remember all those planetary artifacts randomly scattered around the systems? Various devises that, despite being tenths of thousand years old (already being old back when the vasari empire was just being established), are still in working condition, yet are so beyond the tech levels of current races that they can not even comprehend the the scientific principles behind them, much less copy them? The phase inhibitors that all three races mindlessly utilize are a good example of a more 'common' type of derelict - one that even vasari, who are generally acknowledged at having the most advanced understanding of phase space physics, have no clue about its inner workings. They merely managed to reproduce the original devise with their nanites (the only known successful copy of an artifact), but gave up on trying to research them long ago. The inhibitors of other races were acquired by somehow stealing these structures from vasari (according to backstory).
All this practically screams of a galaxy spanning precursor civilization, one that predates all current races by as much as hundred thousand years or more (since even the old vasari empire have no concrete knowledge of them). The civilization must have been widespread, since their artifacts are everywhere, from original vasari space near the galactic core, to human space (which, if its anywhere near Earth, is pretty far away, having taken vasari several thousand year to get to), and may have also been influential of some of the vasari's tech advances.
As with many other sci-fi series, one wonders what might have happened to the original race to make them absent from the entire known space, despite being many thousand years more advanced than either humans or vasari. This is where the theories begin:
1) They were completely wiped out by 'something', which must have been either incredibly powerful, or undergone asymmetric development (focusing on some alternative to normal technology) to take on a galactic civilization. Afterwards, this 'something', having nothing to do after wiping out the last remnants of the original race, gets bored and leaves the galaxy / goes back to wherever it came from / goes into hibernation near the inaccessible galactic core / retreats into phase space.
Many years later, new races have arisen. The imperialist vasari, being the arrogant fools that they are, somehow manage to awaken / make their presence known to this 'something', who then promptly returns for another galaxy wide purge / conquest for resources or technology / feeding spree. They are apparently not rushing, taking their time to spread from the core outwards, knowing they would eventually get the fleeing vasari anyway (unless this entity is entirely mindless, and just goes on about its business not even noticing the vasari).
2) Its the precursors, they are abusive, they are back and they are out to get you.
Long story short, its the original precursors - for whatever reason, they decided to temporarily migrate / go conquer nearly galaxy / go on vacation / another one of dozens of possible excuses to disappear for a while (100k years is peanuts to them). As an alternative, they may just be a bastard offshoot of the original precursors, who nevertheless have their tech levels. Having come back home, they find that a bunch of primitive races have taken up residence in their systems, with the wannabe vasari empire at their head. Not amused, the precursors then promptly proceed to retake what they believe is theirs anyway, curbstomping the entire Dark Armada in the process.
Why its taking so long for such an advanced race to catch up to the vasari is unknown, they either a ) just dont give a damn about chasing them and expand at their own pace or b ) they are very few in number, and dont have the means to spread across the entire galaxy at this time (unlike what is portrayed in regular sci fi, the galaxy is pretty fucking big, around 300 billion stars. Thats 300 000 000 000, whereas the entire TEC takes up a couple hundred systems tops, and the all powerful vasari empire spanned a few thousand. Normal map is 2-4 systems. Feel the difference).
3) The precursors are not related to this 'something' at all, and are just extra backstory. Which I find hard to believe, and this would be boring.
What is currently known about this 'something':
- It appeared deep in the vasari empire space, near their oldest planets, in the territory they considered their core. It did not come from the outside. Possible places of origin - a) inaccessible galaxy core - gravity/heat is huge there, current vasari tech could not handle it so they could not explore than region, and assumed there was nothing inside that could threaten them b ) phase space - it eithier originally resided in phase space (space monsters / psi entity / Chulthu / tech civilization that originated there), or was imprisoned there (precursors sealed their shit in a can / their conquerors there / just got bored of normal space and moved there on their own). Whatever the reason, it eithier wants to eat your brains, or doesnt like you messing with phase space since where they live, and thus periodically goes on exterminatus campaigns. Vasari were doing experiments on phase space tech, and either released the sealed something, or alerted these beings to their presence and they came on their own. Phase inhibitor artifacts may or may not have been a trap, depending on who's attacking the vasari.
- The mass uprising of the vasari slave races is very unlikely. While the rebellion itself would theoretically be possible, there is just no way that it would happen without anyone knowing what was going on. The slave worlds were isolated, had no spaceships of their own, while vasari lived above them on capital ships - anything that tries to get off the planet is immediately pounded into the ground. With their nanites as spying equipment, an empire wide conspiracy is just not possible. The only way for a mass rebellion to take place is if the ENTIRE vasari themselves become infiltrated/controlled (through psionics), but the problem with this theory is that worlds disappeared one by one, there was no large scale uprising as would be expected, everything/everyone outside of the dark planets was normal. Besides, psionics do not work on robotic ships, vasari would have fairly quickly determined what was going on through automated systems/sensors, to put it bluntly you dont mind control someone over internet (vasari dont all have cybernetic implants last I heard).
- The important point is the crew of the entire frigate going mad with fear. Even if the enemy has overwhelming force and you see the entire fleet of your race destroyed in minutes, you dont go insane, it just doesnt happen like that. There is such thing as shellshock syndrome (for those who dont know see youtube vids from WW1), but that's not insanity, and its very unlikely to happen to the entire crew at once. To me it seems that this is a sign of psionics being used on the vasari fleet, the enemy might have gotten the vasari to kill eachother off. So as much as I like the grey goo theory, I wont believe in psychic grey goo.
- Extra-galactic race incursion not likely, as they would have jumped on the edge of the gravity well, the well being the galaxy itself in this case. Not in the center. Advanced space mongols (nomad race) from Milky Way also not likely for this reason, they would not suddenly appear in center of vasari empire.
- Whatever is attacking, it is likely not an ordinary high tech civilization. If they were, they would have caught these vasari long ago, even if the group facing the TEC are just one of many such groups that bolted from the original vasari space in random directions. They have been running for thousand+ years, making lengthy stops to collect resources, and leaving a breadcrumb trail of phase space beacons behind them, that would be enough to both find and catch them. The pursuers are eithier not a tech race, or they dont particularly care about vasari and just happen to be closing in on them while spreading uniformly from the core, or they are a non-intelligent force (or having different kind of intelligence) and do things that seem bizarre to normal races.
- On the other hand, vasari are also not particularly intelligent, since instead of going around the TEC space (which is not that big) and focusing on collecting resources from neutral/dead worlds/asteroids, they insist on plowing right through and getting bogged down and losing 25 years of interstellar travel, as well as people and assets. All to conquer some race they consider primitive, while they dont really need slaves at all.
Anyway, at this rate I can go on for another couple pages, so I'm going to sum it up:
I believe that their enemy most likely came from phase space, has extremely strong psionics and almost total control / understanding of phase space (which would be required to keep the vasari from figuring out what was going on). Once you enter the occupied system, it became practically impossible to escape, regardless whether the vessel is crewed or not. FTL communication (based on phase space physics) doesnt work. The technology level of this entity does not necessarily have to be on par with precursors/ vasari or even TEC, if they have even technology of any kind at all to begin with.
It definitely has some connection to the precursors, and it may have killed hem off through their vulnerability to psi - may not have taken them on in a direct fight, but making them fight each other is a different story. This way, although TEC/Vasari are significantly less powerful than precursors, they have some chance of fighting back now due to the existence of Advent faction psi knowledge. Psi+Phase techs may be whats required to stop it.
It is probably not a conventional race (like precursors or bugs w hive mind), as it does not behave as one - the fact that vasari remnants are still alive after all these years and the method of conquest of vasari space proves that. Or, if it is a race, it just plainly does not care about vasari or any of the other races and just does whatever it is that it does. Or it has a very unconventional way of thinking (horde of alien locusts / phase space entity that normal races cant comprehend ).
It is possible that phase inhibitors were legitimate remnants of normal precursor infrastructure (they may even have been built for some other purpose than what vasari use them for). However, it would be more interesting if these were a trap laid by whoever destroyed the precursors - they assumed that the new races would want to tinker with it (what better way to ensure that something is opened than by leaving a Do Not Open sign on it), but would only be able to figure out enough by the time they are advanced and spread across many systems. At that time, they open a rift to the location of the entity, it comes out and does whatever it is that it does.
Alternatively, inhibitors were built by precursors to slow the spread of the phase space entity, in this sense the phase space was both its strength and weakness.
So as bland as it is, most likely explanation is phase space Chulthu. Or a sentient psychic blob of nanites, if you believe that (I dont).
I would be legitimately surprised of Stardock managed to invent something that is not some variation of the above and would leave no plot holes.
Anyway, feel free to discuss / complain about the length of text.