One of the most interesting things in TES lore for me is the mysterious disappearance of the Dwemer. My theory about it is that when the Gods saw how much advanced the Dwemer had become (they also managed to create a God), they planned something to extinct them forever in a subtle way. Yours?

Not a theory, but the Word of God from the devs; they absorbacided themselves into the Numidium and became its golden skin. From the clan that went to Hammerfell to all the way to Morrowind, each and every dwemer became the Numidium's golden skin, save for YB. The question that should be asked is why YB was the only one not absorbed to become the Numidium?

The case has been closed since...a little after Morrowind, so it's old, just not often known, knowledge.

I think the general consensus is that they became the skin of the Numidium as a result of sticking their nose in things they didn't quite understand. Damn, ninjaed

No, that result was intended. Whatever they had planned after that didn't work out, though, as I don't think they were attempting to become a mythic-scale weapon to be wielded by mortals for mortal conquests. Likely the following stage of their master plan involved Yagrum Bagarn; it'd be a pretty unlikely coincidence that he was in an Outer Realm when Kagrenac did his thing, protecting him from the absorbocide, just because he felt like it.

I thought they wished to become a God, not become his flesh. From what I understand, they didn't really have any control after that. Who would want to just become the skin of a deity and have no control after that, being basically enslaved to the will of a conquest hungry Emperor of man.?

Maybe because Yagrum Bagarn was partly disabled? (has no legs, half of his body is already mechanic). Dwemer constructions weren't absorbed because they were mechanic.

Becoming a god involved becoming its flesh. Their not having control afterwards was why I'd presume Yagrum would have to get involved, as he would be able to complete their apotheosis, being an agent of control with the required intention.

The mechanical thing isn't part of Yagrum Bagarn. It's like a wheelchair, except a spiderchair in his case. Not to mention that he didn't build it until some time after contracting corprus.

right, but thats all they are, its flesh. They didn't become a God, they became but part of what they hoped to make a God. I'd say their intention was to become the Numidium, but not in the way it turned out.