With the majority of the droid armies deactivated, their leadership killed, and the reorganization of the Republic into the Galactic Empire (and the framing of the Jedi as being the root cause of the corruption that lead to the war) the Seperatists would likely have been rolled over by the Empire, or willing joined if their reasons for leaving the Republic were satisfied by the absolute dictator that was Palpatine.
There were of course Seperatist holdouts. Those would be used as the excuse to expand the Stormtrooper corps and the Imperial Navy. They would mostly be crushed within the first decade. Its remains likely absorbed into the Rebel Alliance on its founding (likely later this year in Rebels).
There were of course Seperatist holdouts. Those would be used as the excuse to expand the Stormtrooper corps and the Imperial Navy. They would mostly be crushed within the first decade. Its remains likely absorbed into the Rebel Alliance on its founding (likely later this year in Rebels).