This would make a decent quest line to be honest. You could discover that when the Dwemer ditched, they had gone off to far off ancient lands forgotten/unknown to the other races. And you could also string in the Psijic Order, going off to find them and learn more? It makes sense. The Psijic Order being the most elite mages, superior to the Imperial Mages Guild, and the College Of Winterhold, running off to seek greater knowledge than any men have yet discovered, to find the Dwemer off in... Le'ts say Atmora? The Psijic Order then starts learning, problems rise, the Order abandons Atmora, the Dwemer, being enraged over something then seek them out near Skyrim? And they all go to war. I like this idea. Although it seems a tad bit dry on the magical fantasy side, it seems good. One change though, don't let it take place in Cyrodill. Put it in somewhere different, that was in the older games, or has not yet been released. I would also think it's better that you don't start off in an Imperial/Dominion prison. Make it a joint prison camp, controlled by both of the factions. Let's say you were being taken prisoner by the dwarves to work as their slaves(The Dwarves have some kind of... Addiction to enslaving people). Then while you were being taken to the Dwarves Slave Camp, you were all ambushed, and taken to the Joint Prison? I don't know, I'm just throwing ideas out there.