I'm very sorry, I try not to do fic searches, but this has been driving me crazy!
What I remember is that Elizabeth left Will stranded on a boat in the middle of the ocean, and ran off with Jack (Jack and Will were lovers, and I'm pretty sure Will and Elizabeth were married, but both pirates and wanted Jack, so it didn't seem to matter much lol). Few years pass, Will is a Sorvereign Lord or something like that, of a pirate council (like Elizabeth was the pirate king) and he was traveling with another pirate captain, who was rather pervy and in love with Will (though nothing ever comes of it and they both know that).
Another persona (it may have been Cuttler, can't remember) believes Will to be Ganymede and was the key to a treasure or the sea, can't remember. The others (Jack, Barbossa, other pirates) start believing it too and there's a bit of a battle over the 'rights' to Will.
Also, Elizabeth was pregnant, but only one or two people knew, like Will. They (Will and Elizabeth) also leave with Jack's father when the Captain stops their ship.
I know, I know so vague! But it was an amazing story, and I'd really love to find it again.