They emerged after Oblivion crisis strong and unifed, and attacked Morrowind and took control and its mainland, and have gone completly separated from Empire.With mer vs man war that is coming, both Thalamor and Empire will most likely try to ally with argonians, for they gain powerful ally who controls eastern Tamriel.
What will be argonians( in truth, Hist) decision?
1. Stand beside and watch.This seems very likely choice.
2. Siding with Empire could prove good for them because they hate mer( Dunmer).But at the same time they could once again become nothing more than another region of the Empire.
3. Thalamor, after years of being ruled by Cyrodiil, perhaps they want some sort of payback time against Empire?