I wrote a previous theory encompassing the main plot points of the finale, which can be read here:
Basically, I was wrong about pretty much everything. I thought the first two hours and twenty minutes were excellent, but I'm going to have to dwell on those last ten minutes for a while. No doubt that was the largest plot twist in the series since the iconic "We Have to Go Back" scene. But overall, that was probably the most emotional episode of Lost ever.
There are enough people on this site discussing the big picture and the meaning of the ending. With the last episode of Lost having finally aired, let's take the big pieces of mythology we've gotten and attempt to apply them to the numerous minor mysteries of the series. Right off the bat, let me state that, by trying to explain these mysteries, I am not "missing the point" nor am I trying to take away from the magic of the ending. Also, keep in mind that I do not endorse any of the theories laid out here as fact, I am merely suggesting them. So, let's go:
---Children, Guardianship and Dharma vs. Others---
I stated this in the previously linked theory so let's get this out of the way. Children who were born or raised on the Island are much more likely to be special because of their proximity to the Light. This is not only because of their constant exposure, but because they are more likely to be able to understand the nature of the Island. Jacob tasks the Others with drafting up lists to find special children who have a shot at becoming candidates. The Others probably didn't know the extent of this plan; they likely think children born on the Island are special because of the pregnancy issues.
The Dharma Initiative arrived on the Island to try to understand the nature of its properties. Like the MIB, they were never able to find the Light in the cave; it only reveals itself to specific people, possibly only its current protector. Thus, they found the Light the only way they could, and the same way MIB did; via the underground and the frozen donkey wheel at the Orchid. Dharma came too close to the source of the Light, so they were required to be purged by the Others, just like many groups throughout history have been for the very same reason.
Walt was someone who was thought to be special, but was not. This is why the Others allowed him to leave. The only reason we believe Aaron was special was because the psychic told us so. This psychic later claimed he was fraud, but he also went through a great deal to get Claire on the plane, so it's left up to interpretation. My opinion is that, had Aaron remained on the Island, he would've gained an ability like MIB did, being born on the Island. Anyone that raised him off Island would eventually bring him back, so it had to be Claire that took him from the Island. She would never bring him back so she must be the one to raise him.
It may have not been a helicopter, but Desmond's vision ultimately comes true. Claire was able to reunite with Aaron off Island because of a chain of events that Charlie helped start. There may have been some stalling due to the MIB's interference with things (he took Claire right when everyone was boarding the real helicopter), but this ultimately ended up happening.
---Smoke Monster, Egyptians, and Wonders of the World---
Seeing what was down in the Light cave gave us a lot of information about these particular mysteries. People have already been speculating that the Monster predates MIB because of the stone tablet we saw in "Dead is Dead." Considering the Egyptian writing all over the Island's cork and the numerous skeletons lining the bottom of the chamber, it is clear that people have been going into this cave since the beginning of time. There have likely been numerous smoke monsters and numerous people that had to kill them. There is always the possibility that Mother herself was one of these monsters.
We were never really given an answer as to why MIB was not allowed to leave the Island. Being "evil incarnate" was likely a dramatic overstatement, and so we're forced to believe that his living would effect the Island or the world negatively. This is either because he has lost his personal light to the Island, or because he has taken some part of the Island's heart within himself.
I believe we got the answer to this in "The End." While MIB thought he was destroying the Island out of revenge, the real reason he needed to is because he can not exist off the Island unless the Light is turned off. The Light is what made him and it is likely that the smoke can't survive with it. But turning the Light off made him a normal human again. Not only was he mortal and able to be killed, but he also had a normal body and was completely free to leave the Island if he wanted. Not that it would matter, because the world would be destroyed. But two birds with one stone -- the only reason MIB can not leave is because his leaving would mean that the Light was off, which can't be allowed.
There is no greater significance to all of the ancient structures on the Island other than to show us that people have come (or were brought) to the Island for a long time. Every culture is represented on Lost, just like every history, art, philosophy and science is referenced. This really fits into the popular Garden of Eden theory; while not the literal garden, the Island is the cradle of humanity. All creation myths and interpretations of god and religion are based on the amazing things that people saw on the Island. These supernatural events made possible by the Light appeared to be magical and divine to the early inhabitants of the Island.
The structures on the Island are nothing more than to show us that all of these ancient cultures have seen what was on the Island at one point or another. The Taweret Statue, in particular, has no connection to the pregnancy issues on the Island and is merely a symbolic representation; it's collapse signals the end of childbirth as if by divine intervention. The structures also draw parallel to the seven wonders of the ancient world. The lighthouse is a reminder of the Pharos of Alexandria, the statue is like the Colossus of Rhodes, the Temple is like the Hanging Gardens of Babylon, the stone columns and ruins could have been Greco-Roman like the Temple of Artemis or the Mausoleum of Halicarnassus. The Temple's underground sections are no doubt references to the inner workings of the Pyramids.
---Electromagnetism, Healing Power and the Sickness---
Again, this was stated in the previous theory so let's get it out of the way. The Light on the Island is likely something far more complex and important than merely a pocket of electromagnetism. It could be God, it could be magic, whatever, it doesn't matter. But the closest way to quantify that light and explain it in layman's terms is exotic matter, a black/white hole, or a huge pocket of unbelievably powerful electromagnetism. We will never know the truth, because it is likely something too far out of human comprehension.
The healing powers and sickness on the Island are granted by the Light. While I wouldn't say it has sentience or intelligence, it does have something of a will and a need to survive. It is "alive," I guess. Darlton always said the Island was a character, so this would be it's brain or heart. Every time the Island prevents a character from dying or killing themselves or every time they say "the Island isn't done with you," it is because that is the will of the Light to some extent. All supernatural and time-bending events stem from the Light, as do all the strange "rules" mentioned throughout the show. As shown in "The End," when the cork is pulled out and the Light is shut off, the rules suddenly no longer apply.
I believe the Island naturally heals everyone on the Island unless they are too far beyond saving. It also gives illness to people that attempt to leave when they have not yet fulfilled their purpose, such as giving Jack his appendix problem. Still, it appears that the Light's ability can be tampered with, probably by the smoke monster. Ben and Locke, the two people that were eventually used by MIB to murder Jacob, got cancer and lost the use of their legs temporarily. Ben's cancer made him believe the Island no longer approves of his leadership, and it was later cited by (Locke) as a reason to kill Jacob. Locke's paralysis in both "Deus Ex Machina" and "Lockdown"/"?" lead to events that made him lose faith in his purpose on the Island.
The Sickness on the Island is a mystery with several misdirections shown over the course of the series. When we were first introduced to it, it was supposedly a disease spread by the Others that made people crazy. We can base this off of Rousseau's statements, the "quarantine" on the hatch door, and the vaccines produced by the Dharma Initiative. In season four, we are introduced to two angles regarding the Sickness. One is Desmond's temporal dislodging upon leaving the Island, or a "time-traveling sickness." The symptoms make the victim appear to be crazy and irrational, similar to what Rousseau said. When we were introduced to this in "The Constant," I was thrilled as it seemed like a creative answer to a long-standing mystery, and they never even said the word, "sickness."
However, having seen the final two seasons, it is clear that the Sickness is related to the Monster. It appears that Desmond (and maybe a few others, I will explain in the next section) are the only people that have ever been dislodged in time. In season four, we see the effects of the "cabin fever" that overtakes the crew of the Kahana freighter due to "close proximity to the Island." The paranoia between Gault and Keamy mirrors the tense standoff between Rousseau and her team a few months after their exposure to the Monster in season five. The nature of the Sickness is explained in early season six: Dogen tells Jack that an evil is growing inside of Sayid. If we take what Mother said about the Light being inside every person, we get a clear understanding of what is going on. To be "claimed" is to be exposed to the black smoke, which can somehow infiltrate your body and cloud out your Light. Maybe it blocks the Island's Light from reaching you or maybe it blocks your own Light from resonating.
Having seen the water channeling into the Light at the bottom of the Island should confirm that the healing spring in the center of the Temple is connected to the Light. The fact that the water can become murky is a sign that it's healing can be messed with, like it was with Sayid in season six. When Richard takes young Ben to the Temple, he says that he will become "one of us." I believe this means that bathing in the Temple's spring is a ritual for becoming one of the Others. Bathing in this spring makes you immune to being claimed by the Monster. This validates Rousseau's statements. She believes the Others are the carriers because they are not sick despite being exposed. In reality, it is because they are immune to the Monster's effects because of the spring. We can take this a step further and say that Dharma's vaccines are, in fact, water somehow taken from something similar to the healing spring somewhere else on the Island.
This theory is getting long so I'm going to cut it off. There is a lot more to cover so I will be following this up with a sequel that will build off the elements introduced here, and will cover things like Jacob's cabin, the volcano, time travel, and other things. So, if you liked these posts, please look out for that. Thanks for reading.
I wrote a previous theory encompassing the main plot points of the finale, which can be read here: