Some concepts I have in mind would be (I'm no expert, so please correct me where I'm wrong!):
-Dagoth Ur being assigned to guard the Heart in Red Mountain by Nerevar (or was it the tribunal?)
-The murder of Nerevar by the Tribunal
-The battle for Ald'Ruhn during the Oblivion Crisis and the retreat to Ghostgate
Now I don't know if time travel is lore friendly in TES, but I believe this would be a nice way to portrait some important events of Morrowind in the game. Maybe the player simply gets a vision about the past/future of Vvardenfell while he is dreaming (Dagoth Ur playing tricks on him, showing him how he was betrayed and what will happen should he not ally with Dagoth)
What are your thoughts about this?