Okay. I've read further, and I've got more.
It says that the illithid came back from the end of the time, not actually because the world was ending, but because they were being defeated by an unknown enemy. Those who returned manipulate kingdoms to study the rise and fall of empires, so they can be certain that this time, when they (re)create their own empire, they can build it stronger. It'll be done "right," it'll be permanent.
And that, of course, has sparked new theories in my twisted brain, as well as tying into my old. Follow me, if you will.
The aboleth are one of the most ancient forms of life. Eventually, an offshoot of them becomes not only ambhibious, but actually land-dwelling. Over the span of eons, this offshoot evolves into the illithid.
Of course, the aboleth meet the illithid long before this, since other illithid came back from the future, but we'll get to that.
This original "strain" of mind flayers eventually rises to power and, late in the "life" of the universe, founds their empire. They are defeated by an unknown enemy, so they gather unheard of amounts of psychic energy and send some of their number back in time.
These "out of time" illithids become the mind flayers we all know and love. Hundreds and thousands of generations pass. They study the way empires rise and fall, and they determine that when they found their empire, it'll be better than it was "last" time (even though last time hasn't happened yet).
Then they discover the empire that the original (aboleth-descended mind flayers) are founding. And they're doing it wrong. They're making all the mistakes that the mind flayers descended from the time travelers have learned not to make. And the second strain of illithid realizes that they must supplant the original strain, to ensure the survival of their empire.
In other words, according to this particularly convoluted plot idea...
The unknown enemies that wiped out the illithid empire were, in fact, the descendents of the illithid who went back in time to escape the unknown ememies who were wiping out their empire.
Assuming your eyes haven't crossed, what do you think?

I feel there's some great campaign/story potential here, but I'd love to hear other responses.