There is a civil war in Morrowind? I don’t remember hearing about that, but about Morrowind itself initiating the rebellion I might agree with you now, I was playing Morrowind earlier and one of the NPCs mentioned that if the Imperial legion are recalled to Cyrodil for some reason, that house Hlaalu would have no qualms about fighting for independence or something like that.
House Dres and House Hlaalu are fighting House Indoril. The latter lost any political support it had with the loss of the Tribunal, and so House Dres and House Hlaalu think it a good idea to get rid of the only other House that is particularly loyal to the Tribunal, besides Redoran, which is being assaulted by Nords.
House Telvanni is probably increasing its power on Vvardenfell with no-one to stop it, and will probably become the next dominant force in politics (House Dres will be bankrupt, as they relied on slave labour which is now, officially, banned, and House Hlaalu would have fought a war).
There is also no dominant religion now, and Azura seems to be in the best position to do something about that (she's the only one who'd really care).
Black Marsh has never been successfully invaded. It was incorporated into the Empire by way of a treaty.
It didn't work as there is almost no Imperial presence there, even in the major cities. A shame, because it must have taken a lot of time and effort for the Argonians to sign it
The Empire is a confidence trick. Do you, the famed warrior races of Tamriel, having won international renown for your fighting prowess, consider yourselves and your abilities inferior to those of money-grabbing merchants and diplomats in armour?