Okay, so the Dwemer disappeared when they tried to harness the power of the Heart of Lorkhan, right? Well what if the power of the Heart somehow made them transcend the physical world and become immortal gods?
So when Dagoth Ur was tasked by Nerevar to guard the Heart while he went to summon Azura, Dagoth Ur experimented with it and discovered the truth of the Dwemer disappearance, and wanted to bring the Chimer to the same level. However, by that time, Nerevar had already been murdered by Vivec, Almalexia, and Sotha Sil, and they soon did the same to Dagoth Ur, but not before he could sap some of the Heart's power to make himself immortal. Those three went on to use the power of the Heart to make themselves immortal gods, and established the Tribunal. As punishment for their evils, Azura curses the Chimer to become the Dunmer, and prophesies the coming of the Nerevarine.
Cut to the Nerevarine's time, and the vulgar actions of the Tribunal on the Heart have corrupted its power; now the transcendence requires the subjects to first suffer from Corprus disease, and it must be spread through the Blight. Dagoth Ur still believes that only the Dunmer deserve to transcend, so he builds the brass god Akulakhan in order to drive the foreigners out and spread the Blight to only the Dunmer.