At the end of the mainquest in Morrowind, Azura comes and talks to the nerevarine directly. She tells him that he destroyed the blight, now his real quest to defend Morrowind has begun. And she basically tells you to do what you can to protect Morrowind.
So after that they made tribunal and bloodmoon and the nerevarine did all that. Helping protect morrowind by taking out corrupt Almalexia.
But 6 years later in Oblivion, people mention that the Nerevarine has left to Akavir on a Crusade of some sort, but leave very little detail on the circumstances of his/her trip.
Now we know, within 3 decades after that, Red mountain Erupts, destroys most of vvardenfell, argonians invade, dark elves flee.
We also know that Azura warned her loyal followers right before the red year to get out of morrowind, and left behind the Non Believers.
So we know azura is "good" enough to warn her loyal champions and what not (just like sul from the books) and preserve them as best she can.
Now, lets backtrack to the end of the Morrowind Main quest when Azura says your duty now is "To Protect Morrowind".
So she tells the nerevarine that his next big duty is to protect Morrowind. Yet not 6 years later the Nerevarine LEAVES Morrowind, never to be heard from again.
In Skyrim, its been 200 years and the nerevarine is still gone.
Do you think that Azura possibly SENT the Nerevarine to Akavir to get something to help PROTECT MORROWIND?
I mean thats one of the last things we know she tells nerevarine to do, and then he leaves morrowind not long after.
Do you suppose that Azura warned Nerevarine about the Red Year and the waning power holding the moon above vivec. Do you maybe think that she sent Nerevarine on this Crusade to collect some sort of artifact, or Army or something, and then return to Morrowind to drive out the invaders?
If so, then what is it exactly in Akavir that has the attention of Nerevarine (200+ years of attention i may add) and Azura, and can possibly help towards the preservation of Morrowind as a nation?
This is just some theory im pulling out of my ass basically. But i think it has some sort of Merit. Theres got to be a reason why Nerevarine left the Nation he was charged to defend, not long before it gets destroyed.
Possibly in future Lore, the Nerevarine may return to Morrowind and bring it to its former glory....
Anyway, thats my thoughts on the situation.