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So, we know that the alt. timeline is, in strange ways, bleeding into the OT, and vice versa. Consider that this has been happening since the beginning of the show, and link it to people getting knocked unconscious:
Claire-- S1, lost her memory after the whole incident with Ethan. Locke-- don't remember which season, but did he not begin to lose his ability to walk? Desmond-- drifting in between two seperate realities, not just the past and the present. What he saw in 'The Constant' was the alt. timeline. Charlie-- I'm guessing those vivid hallucinations he had about Aaron come into play SOMEHOW. Sun-- Losing ability to speak English in the OT. Sayid-- Apparent loss of soul in the Alt. T.
There is also this strange mirror motif that we keep seeing:
Jack-- Both on the plane, and when examining his appendix. Sayid-- In Nadia's door. Kate-- The bathroom of the airport, and right before she picks up Claire. John-- Right before he goes to call Jack, he looks in the bathroom mirror. Ben-- In the microwave. Sun-- Before answering the door for Keamy. Jin-- In the restauraunt with Keamy. Sawyer-- In the police station, he then smashes it out of frustration.
I think that the mirrors might be a direct link between the two timelines that we are currently aware of. And, somehow, this is all going to boil down the bleed-through between these two timelines, and possibly other time lines that we may have seen but may not have realized. It seems like all the characters might...just a little bit, be starting to realize the legitamacy of both timelines.
And I think multiple people in the alt. timeline already do-- Martin Keamy included. Strange, that in the process of "killing" Jin, he was taking surprisingly good care of him. We also have his comment about the island, which I've listened to multiple times. Whether it's legit or not, the theory that he is aware of the multiple timelines still stands. He wants Omar to be careful with Jin because if Jin is knocked unconscious, we could experience bleed-through. That's messy. Complicated. And Keamy is rounding up 815 flight members, for what purpose, I'm not sure. Why else would he go get Sayid in the middle of this whole Jin-Sun debocle?
Desmond, we know, is the key to it all-- he is self-aware in both timelines. Hence his strange dissapearance in alt. timeline after his conversation with Jack. Widmore's end goal is linked to Desmond, because I think Desmond is the only one who is going to be able to safely unleash the island's electromagnetic energy. He doesn't need a constant anymore. He is his own, at this point. Disrupting the energy could have some horrific effects on the island itself, possibly, oh, I don't know, sinking it? Meshing the two timelines together?
But, wait, we have to think Jacob and Flocke as well. How does their fued factor into the sci-fi fest that Lost truly is, at its heart? We now know the Flocke cannot pass over water. Well, this leaves me with a couple questions:
1. How did Michael see Christian Shepherd on the Kahana, right before it went ka-boom? 2. How did Jack see his father when he got off-island with the 06?
Idea: The 06 storyline is another timeline in itself. It's all bullshit. Oceanic 815 truly did crash in the middle of the ocean (in that timeline).
The island truly is a cork, holding evil incarnate in. Jacob is trying to stop these parallel timelines from crashing in on each other, because, well, maybe, if they do-- "everyone you know and love will cease to exist."