I'm a longtime lurker to this site but I decided in the waning days of Lost that I would contribute to the discussion. I'm going to try and integrate the best observations and theories others have created along with the synopsis of 6.16 from the screening to create a comprehensive and reasonable theory for the background to Lost.
Let's start at the beginning in ATS. It is clear that the Mother character has the combined abilities and powers of Jacob and the MIB. First, there are several compelling allusions to her being a Smoke Monster such as the river scene with Claudia and the destruction of MIB's village. Second it also seems that she has some of Jacob's abilities to know about people and events occurring outside of the island. She knew that Claudia would be pregnant with twins and it's probably safe to infer that she brought her to the island.
Much in the same way Jacob can seem to escape the island and interact with the outside world to recruit candidates, I think Mother likely anticipated and recruited Claudia's children in order to replace her as the protector. There are other clues that Claudia is not simply an accident to wash up on the island. She is covered in all red while Mother is seen in blue, and Mother has two blankets, white and black, ready for her twins.
Finally, its also obvious Mother is immortal because she doesn't age as the boys grow up.
Getting that part out of the way, we can establish that Mother was the protector of the island with abilities that combined Jacob and MIB. We can combine this with the Egyptian hieroglyphics depicting people worshiping the Smoke Monster to conclude that she probably isn't the first protector and won't be the last. The basic backstory of Lost is an island with some sort of mystical powers that requires it to be protected from people.
In choosing a successor, ATS makes clear that Mother favored MIB. He was likely the Candidate she had in mind, but things did not work out the way she expected. While Jacob likes the island and clings to Mother, MIB wants to find a way out. 30 years after MIB leaves for the village, Mother finds out he is actively trying to escape the island and apparently may be close to actually leaving.
Long story short I believe that at this point she pulls a con on MIB and Jacob. She wants MIB to be the protector of the island but he wants to leave. So she tricks MIB into killing her killing her and gives Jacob some of her island-protector abilities. I think she knows Jacob will throw MIB into the source and MIB will then be, in a sense, the "muscle" on the island since he can kill basically whatever he wants. Jacob's role is then to keep MIB on the island.
What was unified in Mother (black and white) is then split up into Jacob and MIB. One wants to stay on the island, one wants to leave. One seems to have powerful abilities on the island (MIB) while Jacob looks like he can't just turn into a cloud of dust and rampage through everything, but he can travel outside the island and bring people to the island.
This split/conflict is central to the show and is referenced through colors such black v white, ideas such as faith v science, board games, and characters like jacob/mib, jack/john, and widmore/ben. Essentially, I think the point is that both are two sides two a coin needed to complement each other and to fulfill their roles.
Before speculating on what is probably going to happened in the finale based on this spoiler, lets wrap up some other loose ends:
- MIB was likely imitating Jacob and manipulating the Others in order to find a loophole to kill Jacob. Ben was his loophole. This can be inferred when MIB tells the Others how disappointed he is in them, and the fact that the others had never seen Jacob but instead figures like Christian Shepherd who MIB can imitate.
Okay, now lets talk about how Lost will probably end and what it means. I haven't read the script but I think what we know now and the series finale point to a definite kind of resolution. I think Jack will be the new, and only, protector of the island in the same way that Mother was. During the series he has made the transition from science/reason to faith and now seems to encompass both dualities. He has gone from wanting to get off the island to wanting to go back and stay. Finally, in the series premiere Jack was wearing a black outer suit with a white shirt underneath. I think this was meant to illustrate he would eventually shed his outer "black-ness," meaning reason, anger, etc, and eventually become "white" in the sense of faith and acceptance.
This would do well to add to the contrast and grand arch of the show, going from one protector who symbolized both sides together, to two protectors each representing black/white, back to one protector. Characters are transformed, the island is protected, and the internal struggle, conflict, and duality between two different perspectives within each individual is illustrated and resolved.
I don't know what the "alt-verse" is, but its probably some form of epilogue. We'll find all that out Sunday, but I think that the structure I've outlined here is probably the simplest and fits well into Lost's narrative. I think the writes created a simple skeleton like this and then worked the story around it. The black/white conflict and the transformation of characters has always been the central element of the show, and I think this theory fits well with that.
Sorry for the long post; let me know what you think! Thanks for reading!
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