Having played through Tribunal a second time, there was some stuff I was curious about in regards to why/motivations:

-Why did Alma send the fabricants on the city?
-Why did she kill Sotha Sil? Was this all just a big ordeal to frame him and get him out of the way? If so, why did she want Sotha Sil dead so much?
-How long had Sotha Sil been dead? Was him being deceased actually the reason why Vivec hadn't heard from him in so long?

And lastly, what happens to these dead gods? Do they go into the dreamsleeve again? Aetherius? What? Azura seemed to think that Sotha appreciated the fact that he was killed after all.

Almalexia went crazy when she realized her power was waning. She killed Sotha Sil and used his fabricants to attack Mournhold, so she could send the Nerevarine to the Clockwork City and there she would try to betray him as well.

Sotha could have been dead months or maybe longer from what I see.

Yes, thats the reason Vivec had not heard from him in so long.

That doesn't explain why she felt the need to kill Sotha though. Even crazy people tend have some sort of justification.

I think Sotha and Vivec were coping well with the fact that they were losing their powers. They accepted it. Alma did not. Perhaps she thought with the other two god-kings gone she would have their power. I am uncertain of this. Hopefully somebody with more understanding of this can give you a better answer.

She wanted to be wuved, so she wanted to make it so Sotha looked like a traitor, and the nerevarine died trying to stop him. She wasn't the smartest member of the Tribunal, certainly was the drama queen, and an extreme attention [censored].

[censored] be crazy, yo.

She needed people to believe in her power. By framing Sotha Sil for the attack, the people would look to her for guidance and she would become more influential, her plan being to eventually become the soul 'Goddess' of Morrowind. She knew her powers wouldn't last and couldn't cope with it, so she went luney yet at the same time she was coherent enough to try and solidify her place as Morrowind's main religious figure. Had she gotten her way, we could imagine Vivec would have been next.

I think Vivec did say he expected her to target him next.

She pretty much said it herself :

"None may stand in my way. Not you, and certainly not Vivec. He is a poet, a fool. I will deal with him when I have finished with you."