This one I actually like. According to this theory, Annie escaped from the island to get away from Ben and was so intent on hiding herself that she moved to New York and got a sex change. Ben sent Tom to look for her, but when he found her (or found "him") they fell in love. Ben found out and arranged for Tom to be shot by Sawyer on the beach a few weeks later.
The strongest evidence for this connection is that both names "Arturo" and "Annie" start with the letter "A."
(But also stupid).