I'd be fine with a battle with someone never before seen. There's no need for Jolly Roger, Davy Jones, the Kraken, or anybody else we're familiar with to be the boss. They can all easily be involved for story's sake, and they can all be easily used to spice up the game, but for the most part everything has to be left open-ended, with an explanation being around for their existence after you supposedly defeat them.
The first chapter involves just helping Jack, and a second chapter of the sort wouldn't be so bad either. Perhaps just helping him with another task would do--in the beginning, Jolly Roger tells you to give a message to Jack; as well, in the movies, Jack does owe some debt to Davy Jones. Helping him escape/defeat the first and hide from the second would be a good chapter, and all that entails.
Perhaps you could strand Jolly Roger, or defeat some personal bad boy of Davy Jones and help Jack escape Tormenta.
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Otherwise, Barbossa would make a good driver for a chapter, as, with the game taking place supposedly between the first two movies (though it would make sense somewhere before the first even ends), he was supposedly dead.