You would have to choose sides once again in the new quest chain it would go something like (this is just a suggestion), the courier arrives with a letter from which ever side lost requesting a secret meeting with you. At this point you have two choices, 1. Attend the secret meeting, 2. Tell the faction you originally sided with about the meeting.
From that point forward, depending on your choice, will be how the quest goes, if you attend the meeting the loosing side will, explain that the only reason the other side won was because of you, and with your help they can take back Skyrim. You will then start attacking forts around the country until you eventually take back the opposing side’s city. If you side with the winning side you will defend all the forts or cities from attack until you eventually attack their largest camp/fort finishing the loosing side once and for all.
There is also the potential to add a third party to the war the Thalmore, and as the Dragonborn you can broker a truce because of the emanate attack from the Altmer Dominion, somewhere off the coast of Solitude the Thalmore have established a military camp with their warships anchored off shore, and a joint operation between the Imperials and Stormcloaks is required to push them out of Skyrim.
Would this be something that would interest you?
