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What if, on the deck of the Black Pearl, when will shouts across the fighting "will you marry me?" Elizabeth Swan doesn’t say yes, what if she says no? Maybe she doesn't mean never, maybe she means not right now. But suddenly it is too late and it doesn't matter what she does or doesn't mean, Will pauses and he gawps, wondering how this woman could refuse him, and he dies.
But when Elizabeth said no, she didn't mean "I don't love you" she meant "I don't trust you right now". Of course she is enraged, bereft, the man she loves was just killed by Davy Jones' crew.
What if Elizabeth Swan swings over to Davy Jones' ship, what if she fights like the devil, what if she is the one killed? What if, instead of Will Turner, the new captain of the Flying Dutchman is Elizabeth Swan?
She does what she ought to and she takes out their enemy, …, and she vanishes into the waves to the sounds of cheering pirates.
What if, instead of being the love interest payoff for her single day on land she finds what happened to her father and she gives him a proper burial, and, as she does, she knows where her heart belongs? She knows her heart belongs with the young woman she once was, willing to pretend to be a lady for her father's benefit, before all the trouble started. So she leaves her heart there and she vanishes into the ocean, not to be heard from for ten more years.
She gets lonely, of course, being the only woman on the boat, but then she meets Edward Teach and happily listens to his bitching about Jack Sparrow all the way to the locker.
After ten years without a word Elizabeth Swan seats herself down beside Jack in a tavern in Tortuga with a smile and a free drink.