So many words have been spent chewing over the Vanishing of the Dwemer and indeed that mystery has been solved to general satisfaction many times over already. The standing explanation, in brief, is that Kagrenac's Endeavor culminated in the infusion of his races' "golden souls" into a transcendent being capable of breaking the Dragon and, perhaps, yet more.
Yet is it not strange that in his achievement, Kagrenac touched the souls of all Dwemer across (although not, it seems, necessarily above) the world? This very extraordinary fact has been briefly recognized many times in the past and never once, to my knowledge, satisfactorily explained. When Kagrenac completed his greatest work, every Dwemer in existence, excepting a handful of old ghosts and one extraplanar anomaly, vanished from this world. Every Dwemer, yet not a single Altmer, Bosmer, Chimer or Ayleid. The only plausible reason for this must be some exceptional quality within or upon the Dwemer being itself which distinguished it from that of those Merrish cousins. What, then? What set the Dwemer apart?
The Dwemer were not a politically or even culturally homogeneous group. Their totality is known to have been many times divided and even turned against itself, in disputes of http://www.imperial-library.info/content/pocket-guide-empire-first-edition-hammerfell, http://www.imperial-library.info/content/aetherium-wars or even http://www.imperial-library.info/content/chronicles-nchuleft. They were not a united people, and yet they did unite under the collective name of Dwemer and they were united by their shared affinity for reason, logic and doubt in their neighbors' gods. They were united in their love of machines and the strange metal only they could forge. Most significantly of all, they were united in their disappearance.
All other commonalities among the clans and tribes of the Dwemer may be accounted for by mere cultural factors, nothing more in truth than the traditions imparted from Dwemer elders to Dwemer youths. Their disappearance, however, can only be attributed to some quality shared not, or not only, by social education but by some physical or metaphysical part of the Dwemer's vanished whole.
Where did this quality come from? How did it manifest? What did it reflect? This, I believe, is the true mystery of the Dwemer, and one I fear we are no closer to solving today than we were a thousand years ago.