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There are only two logical explanations for the Dwemers disappearance.
The first explanation involves the Dwemer's technological discovery of artificial intelligence. We know about the Automatons but I think that was just a start. The Dwemer created a whole new race of mechanized creatures to serve them. Their creations rebelled and are currently living deep underground and using the Dwemer as Elven batteries like in "The Matrix".
The second explanation is much more likely. We have all heard rumors of the Dwemer airships. I don't think it would be a stretch to believe that they were capable of designing and implementing much more than that. For example, life support systems, complex navigational systems as well as rocket engines and craft suitable for faster-than-light travel. It is this reasoning that i would conclude the Dwemer built a Battlestar and are currently orbiting the planet of Nirn preparing for orbital bombardment of the lesser races.
Can I offer you a drink? How about this expensive prostitute?