There would not be just one main enemy, you could have multiple 'echoes' of the main characters involved. Mannimarco and Zurin Arcturus for instance. Maybe the Star Orphans are against the idea as well. Some possible conflicts. But the objective is the correction of the warp in the west. With the outcome maybe resulting in the Dwemer returning to Nirn. If that is the case I'd like whoever is leading the dwemer to say something at the end like "Were not ready to go back yet, but when we do people will know" Nice and cryptic. Or any other idea that would be fitting is welcome.
It would be up to the developers(and maybe us) to hammer out the details. But the idea is that you are fixing the warp in the west. Since it happens in Aethurius it could be explained that a series of unknown events occurred in the realm of Aethurius and the result was the Dwemer returning. Let's you have choices and a scapegoat in order to fit it into the Lore. It wouldn't be another warp in the west. Could be a DLC that sets the groundwork for a future TES game in which the Dwemer return maybe? Plus who doesn't want to see the Star Orphans(Essentially cousins of the Aedric Spirits) and the Dreamsleeve, where souls are recycled?
http://www.uesp.net/.../Lore:Aetherius
http://www.uesp.net/wiki/Lore:Dwemer
What do you think? Criticism? Ideas? Obvious flaws? Feel free to expand the idea.