I'm thinking the solution can, yes, be the Thalmor, but not directly. Options I can see... DISCLAIMER: I am not some kind of Loremaster, so I'm just throwing out some ideas here. 1. The Thalmor are being used by one or more Daedric Princes, and very few in the Thalmor know this. Boethiah, Mephala and Vaermina would be a pretty interesting supergroup. And you would also have the begrudging help of other Daedric Princes who don't like them. Meridia would dislike Vaermina. Hermaeus Mora wouldn't like Mephala, because Mephala's all about keeping secrets and Mora would want to know them. And Molag Bal is always fighting Boethiah, so if you really wanted his help, you could make a really grey deal with him (his questline would begin in the House of Horrors.) Anyway, once you uncovered this big plan, you'd have a new goal to find out who was working for who on all sides, and the real main storyline would begin as you make allies across the spectrum of the civil war. This would interrupt the regular Civil War questline at basically any stage. You could also side with Boethiah/Mephala/Vaermina, ending with the Imperials AND Stormcloaks as smoking ruins, and you the Dragonborn High King/Queen of Skyrim with a ton of awesome powers. Kill the High Queen AND Ulfric, and have the Jarls trembling beneath your evil feet! Though you're still the lapdog of Daedric Princes, but you may choose to see it differently... Whether the Thalmor would survive as your personal enforcement group, or be obliterated with the rest, would be up to you. Hmm. This sounds a bit like how Obsidian might handle the story. Bit New Vegas. 2. Something more internal to the Summerset Isles, such as the spirits or families of the people killed by Tiber Septim and the Numidium long ago. This could also include the people of High Rock, so you'd have some more in-depth quests related to the Forsworn. Again, the Thalmor are being used here, but not as far away from their original goals as the first idea, and there'd be more agents of the Thalmor who are in-the-know. You could really run with the multi-faceted aspect of why they're so against Talos/Tiber Septim worship. There'd be more examples of "outside, it's political, but inside, deeply personal on a social-familial level." And as the Dragonborn -- especially if you're playing as a Nord -- they'd have a giant reason to despise you. Which would make dialogue trees with them very interesting. Also interesting if you play as an Altmer Dragonborn. You could also play with Daedric Prince alliances, but instead of them manipulating the Thalmor on a strategic level, they're interacting in an isolated, seedy fashion with certain higher-ups in the order. 3. Alduin alone becomes a more uniting common enemy than he is in the base game. This is one option I can see where the Thalmor aren't the pawns of someone else like I've described, and retain the most similar position to the base game. At most you might see more Imperials breaking off with the Thalmor to help fight Alduin.