Hi, I'm writing a story that goes like so...

Essentially Alduin has been defeated, the Stormcloaks have created an independent Skyrim and the Second Great War has broken out once again. The Mede dynasty and the Empire itself has more or less falled with Cyrodiil becoming a land populated by Warlord "Emperors" who all claim the throne. The true Empire is ruled as a city state from the Imperial city by the Elder Council. The Argonians launched a second offensive into Morrowind, fully occupying the province and introducing slavery to the Dunmer, completing their ultimate vengence and trying to spread the power of the Hist to Morrowind. Meanwhile the Dunmer have all relocated to various provinces including Skyrim, Cyrodiil and Solstheim. The Aldmeri Dominion has begun an invasion of Cyrodiil (which is a slow process due to the Aldmeri "cleansing" all Imperial land they take and enslaving the population of men the find) and is, for all intents and purposes Tamriel's new superpower. Skyrim is in the middle of a second civil war (and a huge economic depression) between the Stormcloaks and Imperial sympathizers who, while believing in Skyrim's independence, seek to aid the Empire against the Thalmor. Hammerfell and Skyrim are in an alliance that assures each of aid against the Dominion should it move against them. This leaves four factions in the world: the Aldmeri Dominion, the Argonian Freehold, the Imperial Remnant and the Union of Windhelm (which is comprised of the separate Kingdoms of Hammerfell and Skyrim). High Rock, while still formally an Imperial province, hardly acknowledges this and has devulged into petty feudal kings and princes battling for control of even the smallest amount of land.

This is where the story comes in. Its been 25 years since the events of Skyrim and the Dragonborn, having attempted time and time again to settle down he has lost his family to the constant war that has engulfed Tamriel. Having become disgusted with a world where suffering of such calibre is simply accepted by the Gods, the Dragonborn makes it his goal to alter the reality of the universe and bring all supernatural beings and Aetherius down to the mortal level of man. He intends to do this by using the Eye of Magnus (which is in this fiction essentially plans that Magnus used to map out Nirn), the Heart of Lorkhan and Lorkhan himself (who harbors vengeance against the Gods) to, in simple terms, turn Aetherius into another Mortal plane, like Nirn. One where all the Gods are no longer immortal but simply men. Now the DB does not understand that the Gods (at least the 9) are already dead and therefore part of the wheel (and therefore the tower). His actions would end all chance of immortality for the elven races and begin a new golden age of dominance for man. The DB also does not understand that his actions would so alter the fabric of the universe that it would awaken the Godhead and end the entirety of the universe. The story will follow Vivec, the Nerevarine and Sheogorath/the CoC as they attempt to stop the end of the entirety of existance.

Its complicated and I can't be sure it's all lore fitting. If any of this seems off or so anti-canon that it can be made to work then I would love any heads up. Also, if any lore buffs have suggestions I'd be happy to listen. I undertsand CHIM and Armananth to a degree but its very complicated nontheless.

Youre free to do whatever you want in your own fanfiction story.
Personally I dont think it very likely that the Argonians will invade Morrowind again or enslave the Dunmer, its not their style.
But its your story.

The first thing that caught my eye was the same as Merari's point. The Argonians already invaded once. It wasn't like they were pushed back; they left when they felt like it, as far as I know. My guess is that they acted in the same way that the English acted in the Hundred Years' War, with an invasion aimed at sack and destruction, not conquest. I doubt they would happy ruling over a territory so far from the Hist and the territory that they are most familiar with. That's not to say that they don't invade again, but they wouldn't do it for conquest in my opinion.

I just want to clarify that your Dragonborn intends to make Aetherius into a second mortal plane, or perhaps merge it with the first one. The thing is that creating a mortal plane requires limitation. Aetherius is by definition infinite; I don't think anyone can create a mortal plane of ALL Aetherius any more than one can fill all of real-life space with matter. And even ignoring that, Creation required the gods to give of themselves. If the Dragonborn can't wrangle up some willing Daedra or Magne Ge to sacrifice themselves (which will be especially difficult since the Daedra saw the trap the first time around, and the Magne Ge learned from experience that it was something they wanted to avoid), I don't think there will be any means to create a new mortal plane anywhere, let alone Aetherius (where the Magne Ge may be able to manipulate things, but the Daedra would not be able to, I would think).

The notion of limiting Aetherius and making it mortal has never occurred to me. I don't know if my concerns are really deal-breakers for your plot, mainly because I don't think the idea has ever come up before. But I would make sure that you make sure that you understand the mechanics of Creation, and I would also determine whether or not you want your Dragonborn to have a chance at success, or if you just want him to try to do the impossible in order to make his observers sweat and worry.