I don't have all the details of this theory worked out yet, but having went back through the first 3 seasons of lost, i noticed something very interesting in "Man behind the Curtain." Did anyone notice what Richard Alpert was wearing when Ben first saw him in the jungle as a boy? And did anyone notice what "Jacob" was wearing in the cabin when Lock caught a glimpse of him? Jacob appeared to be wearing a Nineteenth century outfit that looked much like a captain's outfit. Alpert was also wearing what looked to be the outfit of a crew mate. Hanso somehow makes it off the Island with a diary of their adventures. So I think basically something happened, like a mutany of sorts, and Captain Jacob was killed, possibly when Dharma took over. This explains why Alpert has never been leader of the others (he is subject to Jacob) and why he is so fascinated when people begin to hear him and see him. I'll have more details later, but this is an interesting idea. Penny for your thoughts...
Charlie
Theory by Charlie Bailey
Charlie
Theory by Charlie Bailey