First part of this theory is here:
Let's get right down to it:
---Volcano, Evil Incarnate and Rousseau's Charts---
Ever since season three, people have been wondering about the volcano on the Island and the writers saved the info on it for the very end. When Desmond pulls the cork out, the source emits a bright red light with fiery sparks. This is the volcano on the Island, or at least one of them.
Considering we saw the afterlife and a possible heaven in the flashsideways world, you could very well take what is under the source to be Hell itself. I'm going to offer a less spiritual explanation, but in no way should this take away from your own interpretations of evil incarnate. And if I'm going to jump the shark in these posts, it would be in this section. I'm not crazy!
Other theorists on this sight have given explanations for the Light being unique matter, leftover material from Big Bang, or God itself. Regardless of what you believe, what I take from these theories is that the Light is the essence of life itself and to extinguish it to bring death upon the world. But seeing as the cork is man-made and covered in Sumerian text, one must wonder how it was being plugged before humans arrived on the scene.
Suppose this: After the (God/Big Bang/etc.), this Light source ends up on the planet Earth. Maybe there are similar lights on other planets, I don't know. As we know, before Earth was a planet of blue oceans that could sustain life, it was infernal and uninhabitable, covered by seas of magma and erupting volcanoes, noxious and acidic oceans and a toxic atmosphere. Sounds a lot like hell, doesn't it?
A red light lived in a cave somewhere, bearing witness to this hellhole until, by design or by chance, the light was corked. Maybe a rock fell on it or something, the point is that it was not deliberate, it was natural. With this natural cork in place, the volcanoes eventually calmed, the magma receded, and the world slowly moved towards the green and blue planet it is today. Simplified: the corking of the Light is what paved the way to life existing on Earth.
Eventually, humans come along and find this natural cork. They wonder what it is and pull it out, and suddenly the end is nigh. They realize the importance of this place, build a man-made cork and it becomes the very first button to push. The long line of Island guardians starts here. So, if you want a literal definition of evil incarnate, what would happen if the monster leaves the Island and the Light is uncorked, I would answer: all the volcanoes of the world would erupt, along with earthquakes and any other natural disaster you can think of. The world would return to the way it was millions of years ago, before life began.
---Rules, Ash and Jacob's Cabin---
We know that the volcano on the Island has erupted before. This is where the ash used by the Others comes from. There are many theories stating it is metallic dust, grounded Banyan trees, the remains of Jacob's predecessors, or powdered smoke monsters. But back on that commentary for episode 3.20, it is heavily implied to be volcanic ash and I'd say this seems to be the case after seeing "The End." We know that the Light repels MIB and prevents him from finding or accessing it. If the ash came from that red light under the cork, it would make sense that it can do something similar.
If the volcano ever erupted, I think we know where a lot of that ash ended up. On Rousseau's maps back in season one, she has an area shaded out as the "Dark Territory." We know that both the Black Rock and the Temple reside in this area. I think that it's most notable attraction, however, is the Source itself. In the event of an eruption, the fields and trees would have been covered in repellent. This is also why the smoke monster is most active in this location; not only does it contain the Temple he lives in, but he can also feel that the source is somewhere nearby.
The rules are the most "magical" of any of the mysteries on Lost, and I had hoped they would be a little more grounded in reality. But a key piece of information was given to us in the series finale; when the cork is pulled out, the rules lose their effect. In this aspect, the Light is the fabled "magic box" that Ben talked about in season three and four. Mother and Jacob were both guardians of this light, and they could make up whatever rules they pleased. Still, it doesn't seem like this power is limited to guardians of the Island. MIB wanted nothing more than to leave the Island, and the wheel he stuck into the source does just that. Jack also wanted to save his friends, and many have been quick to point out the similarity between the source and the light in the flashsideways church. Make what you will of that.
An important aspect of the rules is that they make very clear distinctions regarding cause-and-effect. MIB was allowed to put a bomb in Jack's backpack and send it with him aboard the submarine, but the bomb could not kill them unless one of the survivors actively tampered with it, causing their own deaths. The ash works the same way. In "Sundown," the hippie guy clearly says that Dogen was the only thing keeping the monster out. He is the one that ordered the ash circle to be put down, so with him dead, the circle becomes useless.
This explains what happened at the cabin: it was always MIB. The rumbling in the cabin after Locke turns on the flashlight is quite similar to the monster's arrival in "The Shape of Things to Come." When MIB said "help me," he is only referring to leaving the Island, and he really only said it to play Locke and Ben off each other. He was never trapped. Even if the ash wasn't broken, he could still travel back and forth simply because whoever put the ash around the cabin was either no longer within it or dead.
The cabin was built in the 70's by Horace Goodspeed. After the Purge, the Others seized control of it and have been using it ever since. Yet, Ben is the only one who knows where it is and Richard has never taken Ben to see Jacob at the statue. My take on this: Jacob has never lived at the cabin. It makes no sense for Jacob to have lived at the statue for centuries only to hang out at the cabin after 1992. As a child, Ben's mother appeared to him and said he was "not ready yet." This is the MIB. As his plan to manipulate Ben and Locke spans 50 years in time travel, this was likely another piece of the puzzle. At some point after Ben became leader of the Others, he saw his mother again. She led him to the cabin, claimed to be able to speak for Jacob like she did with Locke, and that's the end of the story.
I don't know why the cabin appears to travel around the Island. It might have been a hallucination, it might have been that the cabin got unstuck in time. Maybe the real cabin died, and the one we've been seeing is the smoke monster, I don't know. But Ben says that Jacob (MIB) is a "man who summons you." When the cabin appears to Hurley in "The Beginning of the End" is probably what a summoning looks like.
---Constants, Variables and Time Travel---
The time travel subplot was among my favorites in the series, so it was a shame to see it all go to waste when the flashsideways was revealed to be purgatory rather than an alternate timeline. The events of "The Constant," namely traveling between 1996 and 2004 seemed to be setup for "Happily Ever After," where Desmond travels the between Island and LA X timelines. Having seen "The End," there isn't much to say about this topic, so I'll save it for the last section in this post.
Desmond is the only variable in the series. Faraday thought he was one and it took his death to prove him wrong. As I stated in the previous two theories, whatever happened happened holds true without the possibility of being interfered with unless you manipulate the Light itself. In these cases, it may be possible to change your fate, but not without the cost of creating a paradox or smoke monsters. Desmond's future flashes came from his exposure to the source during the Swan discharge. Using them, he was able to create events that were not predetermined.
Earlier I mentioned the skeletons down in the Light cave; I believe these people are not previous smoke monsters, but previous variables like Desmond. These skeletons are the guys that, for some reason or another, are "uniquely and miraculously special." They are the ones to pull the cork out, and subsequently, many of them died. We saw what happened with Desmond. After accomplishing his task, he was sprawled out on the floor and zoning out. Had Jack not saved him, he would have joined the other skeletons in the cave.
All supernatural events stem from the Light and MIB was not the first smoke monster. Assuming these are true, what is going on becomes clear. Everything on the Island occurs in cycles. Usually, there is just a passing of the torch between protectors. Occasionally, an anomaly pops up; a smoke monster. In the event that this happens, the Island introduces a game changer, a variable, to cancel it out. So, every body down in the reflecting pool corresponded to a smoke monster that was created during the Island's time.
---Annie, Libby and other Unresolved Characters---
For this section, I'm going to draw on my four and a half years of reading spoilers and try to explain some of the aborted storylines on Lost. Most of the archives on this stuff were deleted when Lost sites started banning spoilers after lostfan108. Thus, I have no hard evidence so take this at face value, although if it helps, I'll say right now that I have no intention of lying. If you've been reading spoilers for a while, you should be able to recognize and verify some things.
Let's start with one of the biggest little mysteries: Annie. By far my favorite theory about Annie is that she grew up to be the love of Ben's life. Eventually, she got pregnant on the Island and died in childbirth. This mirrors the death of Ben's own mother, explains why Richard says Ben is obsessed with "pregnancy issues," tells us why he is so fond of the doll she gave him, why he kept Alex, and why he brought Juliet to the Island, not to mention how poetic it is. The writers stated that Annie was of huge significance to Ben's character, but in late season six, stated that she probably left the Island a few years after meeting Ben and a little bit before the Incident.
So, why the change in storyline? Here's my theory: If anyone remembers, in early season three, we had no idea we were getting a Ben flashback. However, all the info we got pointed to the season three finale being a "Dharma centric" episode. "The Brig" was also labeled as Sawyer centric, as Locke's flashbacks were on-Island so everyone thought O'Quinn was shooting scenes for the present time storyline. Anyway, after "Strangers in a Strange Land" aired, the producers got the okay from ABC to announce an end date. Suddenly, the Dharma centric stuff was moved to episode 3.20 and the finale was being billed as a huge game changer. This was "Through the Looking Glass."
If you notice, "The Man Behind the Curtain" has a lot of gaps in its flashback story. The Purge is never really elaborated on, Annie never shows up again, stuff that appears in "Dead is Dead" doesn't appear here, etc. I believe the reason for this is that, like Desmond in season two, Ben was supposed to get the two hour season finale as his first centric episode. All of the Annie stuff that would have been covered was cut and saved for a later date, and they never ended up getting back to it. When the end date was announced, they had to introduce the flashforward, so his story was trimmed and stuck a few episodes before the end. Sad if it's true, I would have liked to see this stuff.
Next up is Libby. Why she was in the mental institute is probably explained by the simplest possibility: she went a little crazy after her husband died. Now, back in season three, the writers said they killed Libby off without showing her story and they had a masterplan for getting back to it. Yeah, ok. They specifically said that Libby being connected with Dharma was "not barking up the wrong tree." What I gather from this is not that Libby works for Dharma, but rather she works for someone and wasn't who she seemed to be. The most obvious explanation is that she works for Widmore. The theories started popping out about her right after "Flashes Before Your Eyes," where people started connecting the dots and saw that Widmore send Desmond on that boat race on purpose. If this is the case, than the mystery behind Libby is simple. She was just some middleman payed off by Widmore to give Desmond the Elizabeth.
Now, why the writers killed her off so early, I don't know. They claimed that it had nothing to do with Watros' DUI and said it was because nobody would grieve for a character like Ana-Lucia. This could be true but it seems a bit overcomplicated for something that simple. Considering the episode right before Michael's shooting was used for a Rose and Bernard centric story, one must wonder why they didn't just give us a one-hour Libby flashback the week right after "Dave" if they knew they were going to kill her. Confusing stuff.
Finally comes Mr. Daniel Faraday. With this, let's talk about the stuff the writers cut out from season four because of the writer's strike. Two or three hours went missing from season four. Now, even though Sawyer and Claire didn't get flashbacks that season, I think that would have happened anyway. Those two episodes were dedicated to the freighter team's flashbacks. Now, considering Miles' relationship with Pierre Chang and the fact that Charlotte was killed so early in season five, I'd say it's more likely that we missed a Charlotte flashback in season four rather than a second Miles episode. But one of the missing ones was definitely for Daniel Faraday.
Now, Faraday got two centric episodes in season five but it still wasn't enough. We really only touched on what his experiments at Oxford were about. The biggest problem is that "Desmond will be my constant," was never touched again in the entire series. Here's my theory: Daniel was always going to die in season five, but his centric episode, "The Variable" was actually going to be in season four. It would have been a true sequel to "The Constant" rather than just a sequel-by-name.
Early season four, Faraday says the light "doesn't quite scatter right." In "The Economist," he does a rocket experiment to test the time dilation on the Island. This story is never touched again. He and Charlotte trek over to the Tempest station, and soon after, the writer's strike occurred. We know he's studied Dharma all his life, and his notebook his filled with stats for the Orchid station that was introduced that same year. I believe the writers were setting us up for a late-season Faraday episode where he put the results of his experiments to good use and time-travelled himself. We saw what Desmond could do, and he didn't even know what was going on. Imagine if Faraday did it? I wonder what he could have accomplished.
This post went overtime again, so quick thoughts, then I'll leave. Another season four aborted storyline was the 815 at the bottom of the ocean. In spoilers, the writers said that two different explanations will be given, one of which will eventually become true. When they ran out of time, they just had Tom say Widmore put the plane there in "Meet Kevin Johnson." The other explanation that they abandoned was the one that Naomi started in season three. The plane at the bottom of the ocean was, in fact another 815 that crashed in the ocean because the Island wasn't there. This would have introduced the idea of parallel universes, time travel, etc.
Last thing: Eko was supposedly given a four season arc. But this show was always about Jack and Locke. Locke was the one dragged in the whole by MIB in "Exodus." Locke was always going to be the one that MIB uses. While Eko would have been a rival for a while, I believe his storyline would have ended the exact same way; the monster realizing he can't manipulate someone with such strong conviction and simply offing him. So we got to see Eko's story in it's entirety.
Third post will be the last. Thanks for reading.
First part of this theory is here: