The Empire wasn't disbanded after the command died. There were still huge fleets around the Galaxy. The third in command (another Grand Moff but I can't remember his name) took over. Also, the emperor was still alive. He resurrected his soul in the body of an old clone trooper.
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Is that even cannon anymore
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Yeah, but what happened to Vader's fist (501st) after the movies.
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I can't entirely remember, but I believe they served the new command as marines. They would go in first, wipe out any rebels and hold down whatever area they captured until a new legion would arrive.