To my understanding, Dagoth Ur used Blight in Morrowind to possess the citizens. Miraak, who is only an antagonist in the solstheim related DLC; taking place in Morrowind, also somehow takes control of the people. Miraak died one thousand yeard before the events of dragonborn (according to the dunmer at the earth stone), but Morrwind takes place, I believe, 400-600 years before. Miraak never really died, and has an ability to travel from apocrypha to Tamriel in a "state of flux." He may have observed the actions of Dagoth ur and the Nerevarine, learning how the Blight is contracted, and using it, with a new source, being the elemental stones on Solstheim.
If I'm wrong, tell me, I barely know what I'm talking about.