How can you destroy the rebel empire? I have taken over forts, armies and destroyed navies. There is only one more faction left (Brittania) and they have the last territory. Do the rebels continue to fight even though they have no armies or civilians to fight with?
No, you cannot destroy the Rebel faction in the way that you can destroy normal factions.
Generally, a faction is destroyed if they lose all of their settlements or if all of the men in the family die.
The Rebels are not destroyed. They represent forces and settlements not allied to any of the major factions. It may be possible to eliminate all Rebel forces and settlements on the map, but more Rebels could appear later.
Destroying rebels is hard. Rebels cause problems. they can take over a town that you have taken mostly those towns near ports. so keep them away by strengthening these towns with large armies mostly the cavalries