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I'm sure some of you have read theories on here that Mother could also be a smoke monster, which would explain how she killed the entire village, and filled up the well so quickly (impossible for one human to do this).
Anyways, let's assume now that she is similar to MIB in every way. This would mean MiB is the actual protector of the island, just like his smokey mother was (let's called her Smother, hehe). This would also mean Smother (although her body is dead, like MiB) is a spirit of some sort who can shape-shift into dead people. Which leads me to this theory... she is the main antagonist in the overall plot. She is still manipulating things on the Island for some end or some purpose. She is the one who showed up to Hurley as Isabella, and to Boy in Black as his real mother (also part of her long con for him to eventually become Smokey). She is also the Jacob that is showing up to Hurley, as well as showing up to Hurley as Michael. She is ALSO part of the Whispers. I think ALL the whispers are all the island leaders who were killed (like Smother) but want to leave. Now I know Michael said the whispers are "those who can't move on", but this statement would actually still hold true if my theory is correct.
I think her long con, which spans even past the six seasons we have witnessed, is for MiB to find his way off the island so all the other past leaders can follow because they are all sick of being there and want to leave too. Who knows how many past leaders like this there have been, possibly only a few, but this would still be enough entities present to create the whispers.
This theory ties everything together, and answers many questions much clearer than what has already been vaguely explained. It would explain visions of dead people that we know aren't MiB. It would also explain the why of everything that is going on.
Please discuss and modify if you wish, I just wrote this off the top of my head without much editing. I look forward to reading critisism so the theory can be tweaked to make sense, or even destroyed. Either way is good. Cheers.