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All of these I will present as "mini-theories" if you want to call them that. Meaning I'm speaking of them as if they are true. I'm putting this disclaimer up because I know Lostpedia decided to crack down on spoilers, and this is me saying these aren't spoilers. I'm just thinking out loud.
- CHANGING OF THE GUARD -- The chant that Jacob's mother used was to (for lack of a better word) "bless" the wine, thus making Jacob protector of the island. The same chant was used by Jacob to bless the water in the stream before Jack drank it, thus making Jack the protector of the island. I think a very significant point here is that it was never the wine that sealed the deal, it was the words said for it.
- META-CONSTANTS -- There is no doubt after seeing this that Desmond is the link between the two timelines. Desmond is acting as a 'recruiter' of sorts to get the sideways doppelgangers together. It appears that Hurley is now fully aware of the other timeline now as well. The idea of a constant is alive and well, and is now on a more grandiose scale. In "The Constant" it is revealed that Penny is Desmond's constant. The same basic concept is being applied on the holistic scale now. Penny is Desmond's one true LOVE, thus he is connected to both the present and the past in his time flashes. Love is the all-encompassing 'meta-constant' that connects the two timelines irrevocably. This is why Hurley (and arguably, Libby) are now fully aware as Desmond is. They both have reconnected with love in the flash-sideways.
- THE DEAD -- Jacob stated that once the ashes burn away and the fire goes out, he will be gone forever. This is not to say that Jacob is "alive" again as his ashes are burning (some have suggested this), but that burning his ashes is how he will be able to return to the source. I will unpack this:
- We now know (via conversation between Michael and Hurley) that the whispers represent the people who have died on the island, and that they are trapped there. They are trapped on the island because they have died in such a way to prevent their bodies from being at rest.
- This applies to Jacob as well. Jacob was killed and burned, but his ashes were not burned entirely, thus he is still on the island. Once his ashes are entirely burned, he will no longer be stuck on the island, and will rest in peace. (NOTE: I do not mean to say that burning people until their ashes are gone is the ONLY way for people to leave the island after death. It is merely one example of how to properly do this. Libby was properly buried, hence she is no longer on the island. Boone, and Shannon too.)
- THE SOURCE -- So where do people go after they die on the island? Where will Jacob go after his burn and he is unequivocally gone as he says? Back to the Source. The island is the cork that keeps the Source separate from the rest of the world. It is the soul of the world, and a part of it in each of us is what comprises our souls. Once the remains of someone is properly taken care of, the part of the light within them returns to the Source. The act of Jacob throwing his brother into the Source killed him, but returning him directly into the Source short-circuited the system, thus turning him into the smoke monster. His brother, i.e. the Man in Black is, for intents and purposes, dead - but because of the circumstance of his peculiar death, for him to rest eternally he needs to return directly to the Source because it is where he came from. The problem with this is that MiB returning to the Source will cancel the system out, thus negating the Source and obliterating all of existence with it.
- SIGNIFICANCE OF THE FLASH-SIDEWAYS -- The flash-sideways world is the start of our Losties being rewarded the second chance that they deserve. Desmond, being the 'recruiter' is charged with the task of uniting the consciousnesses of the doppelgangers of the flash-sideways world with the consciousnesses of the core characters (Losties) through various means (I do not imply that love is the only means of doing this, it is simply the easiest way to accomplish this task. We've seen examples of other methods working. Case in point - Desmond running down Locke, beating up Ben, etc.) Once all of the characters in the Flash-sideways become aware of the other timeline, they will be fully aware of their other lives, thus they may continue living them. This eliminates the need for the characters to exist in both timelines as they are one in the same, so now whether the original characters die or not doesn't matter - once Jack and the others defeat the MiB and die doing so (which I believe they will), they can still live on in the other timeline that's been created for them. The Losties, after all that's happened, have finally come to see the errors in the way they lived their lives before the island. The ones that have redeemed themselves have been awarded a second chance in the Flash-sideways.
Thanks to anyone read through my thoughts and theories. They're probably not perfect, so I'm happy to receive criticisms, and corrections. Comments welcome!