Board Thread:Lore Discussion/@comment-129.21.143.199-20130911211744/@comment-75.75.80.173-20140505061233

It could be that the Emperor was assassinated, a High King was was elected, but vied to get someone into the Empire on their behalf, or perhaps the Dragonborn was involved in some plot to gain the Empire's throne.

Either way, the people of Skyrim likely had some economic disaster alongside the damages of fighting vampires. Any dragons left likely continued expansion  ( possibly resurrect ithers without Alduin ), leaving Skyrim to likely leave the Empire regardless of who won the Civil War.

Thalmor probably would also try to set agents to rule the Empire & seek to continue their plan by attempting invasions of Hammerfell, High Rock, & Argonia.