Not hiding, just existing. It’s canon that the Empire didn’t just die with the Emperor, it just lost its figurehead. But it was a huge organization that ran with a lot of momentum and the war continued on in various forms for a very long time.
The war probably got a lot worse after Endor, with hundreds of Admirals and senators vying for the emporer’s throne. I’m thinking it was like Game of Thrones, but with lightsabers.