It's true that most of the Disappearance of the Dwarves article is derived from Morrowind. I hunted down everything I could find on the topic, talked to Yagrum, Baladas, Divayth, and did the Trebonius quest (with the amusing resolution). But there are 2 very big flaws in the DoD summary: the in-game interaction of both Vivec and IIRC Azura. Both of them directly tell the player that they don't know what happened to the Dwemer. Neither of them, especially Vivec, have any reason to lie (except through convoluted logic to support the IL). So we've got a situation where Vivec in-game contradicts Vivec at the IL. That's a serious flaw, IMO. It's possible that different writers worked on the dialog, and that they had different ideas about what happened, with MK trying to "win" his viewpoint through posts at the IL. It's possible that he changed his mind, or that something else happened. But I personally think that if the IL contradicts in-game content, the in-game content wins.
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I dont really recall Azura ever mentioning the Dwemer except with 'lost Dwemer's folly' at her speech at the end of the main quest.
I could be wrong though, its been a while since I played the game.
Vivec only says he senses no presence of them, in any world.
At least when it comes to Vivec I dont think there is a contradiction. He could be telling the literal truth, but not the whole truth, in the game.
If the Dwemer had become one with Numidium at the time Kagrenac struck the Heart, it would be true Vivec could not sense them, they would be gone.
Also, Vivec is a poet, and a liar.
When in-game he says he did not kill Nerevar, he is lying.
The truth can be learned from a hidden message in the Sermons, that states that the god Vivec did not kill Nerevar, but Vivec the man did.
"The Secret of The Lessons
If we take the numbers from sermon 29, use them to take out words from appropriate sermons and put them together, we will get a secret message:
"He was not born a god. His destiny did not lead him to this crime. He chose this path of his own free will. He stole the godhood and murdered the Hortator. Vivec wrote this."
Also, if we take the first letters of all the paragraphs of sermon 36 with the exception of the last one, we will get another secret message:
"FOUL MURDER." "
(Source: The Imperial Library)
The story of the Dwemer attempting to become the golden skin, golden mean, of Numidium also makes so much sense when you look at what the Heart is, what the Tools were for, how divinity works in TES, even the Thalmor in Skyrim, who are via very different means attempting to achieve the same as the Dwemer were.
Numidium was supposed to become a god.
Tiber Septim used it to forge the Empire, it created the Warp in the West, Dagoth Ur had plans to make it a god in his own image as Akulakhan, apparently that is what the robot is for. To be a giant time and world changing god.
Is it then so far a leap to make that the Dwemer, or Kagrenac at least, intended for his entire race to become that god?