I’d like to welcome my cousin Michelle, who does such an awesome job summarizing her theories on Lost and presenting ideas on some of the unanswered questions, that I’d like to share it with you guys. Enjoy!
The earth exists as a living thing and there is a point where all the energy that allows life comes from. This is the island. It is the ‘heart’ where all the energy, life force, (electromagnetism) exists. This was the light that had to be protected. Just like in acupuncture there are certain parts of the body that when pricked can stop pain etc. There are hot spots on the earth where there is more energy than others. This is what the psychic was talking about to Rose and Bernard when they were looking for a cure for her cancer. She said that she couldn’t be cured there but there was another place that she could (the island).
The island is also where all time exists or comes from like The Dark Tower (Stephen King’s series). Time does not pass there at all or in a different way that is why babies could not be born. At certain points in our time (when the series began for instance) the island appears. Like in Star Trek 2009, Nero had to wait years for Spock to come out of the wormhole, when the time periods lined up. This is why it was necessary to build the pendulum in the church to find out what time and place the island would appear. The church itself may be a hot spot, which is why the pendulum works.
The island does exist physically, it is real and the time our characters spent on the island did happen when they were alive. People (like Widmore/Dharma) believed in its existence and were able to create the pendulum to find it. Just like people have always been searching for Shangri La, Eden, Fountain of Youth etc. Once they found the island they discovered the energy and electromagnetic effects that it had. They began doing experiments to see if they could harness this energy. When they realized the dangers involved, they created the hatch/station with the button to help contain places that they accidentally drilled/released.
They also knew about the island being the center of all time (or that it was only existing at a static point) that was where the bunny experiments came from. They also experimented on other animals (hence the cages) including polar bears. Widmore had a picture of a polar bear on his wall, so he was the one who brought them to the island.
They also began doing psychic experiments. That’s why they wanted Walt, because he had some kind of psychic ability. There were also other people who had psychic abilities like Milo being able to hear dead people and Hugo see/talk to them. I think the psychic storyline was a red herring, something Dharma hippies in the 70′s would be into or simply something intesting to add. The writers incorporated many different philosophies, mythologies, religion, science and that would include things like psychic abilities and numerology.
Desmond is special because he is able to live through exposure to large amounts of electromagnetism. I think it could be like a natural immunity or like why some people are able to live after being hit by lightning. Widmore knew about this and that’s why he wanted to bring Desmond to the island to help him harness this energy. This is also why Desmond was the only one who could open the cork of the island because it was the place of largest concentration of electromagnetism. The cork was keeping the energy from ‘exploding’ and destroying the island and the earth. When Jack went down to put it back, he knew he wouldn’t survive the exposure, that’s why he gave the duty to protect the island to Hugo. The whole point of taking the cork out was to allow Jack to kill the smoke monster. During that period, the island was no longer providing its healing powers so the monster became mortal in Locke’s body. Jack had to put the cork back to save the world and contain the energy again. This was his destiny, which he finally realized.
Like Adam and Eve, Jacob and the Man in Black (and all the protectors of the island) were human. The island has been around forever-exists at all time- that is where the statue and hieroglyphs came from, ancient people that had found the island.
When Jacob put the Man in Black into the light, it killed his mortal body (from exposure) but it released his soul (Terry O’Quinn’s theory on Jimmy Kimmel), which became the black smoke. The smoke was often referred to as the security system; this could be a reference to the fact that he was originally one of the people to potentially protect the island. Why he became smoke, I’m not sure of but would suppose it had to do with the fact that he was ‘bad’, had just killed his mother. He also was not ready to ‘move on’, he wanted to live. He didn’t go into the light voluntarily, he was murdered by Jacob. He always also wanted to leave the island and the only way that he could do that was to become mortal again (by possessing Locke’s body). He was the one who was always speaking to Ben, not Jacob and he was the one who convinced Ben to kill everyone in the Dharma Initiative and to kill Locke and bring his body back. Like the devil, he would promise things like making Ben head of the island, giving Sayid Nadia back etc. He didn’t plan to keep these promises; he just wanted to use them to get off the island. He also hated the island and wanted to destroy it. He didn’t know that destroying the island would destroy the rest of the world (that he wanted to return to), that is why when Desmond released the cork, Jack told Locke that they were both wrong about what was going to happen.
The black smoke was the one that was appearing as dead relatives. He wasn’t physically taking form but he was able to hypnotize or make Jack and the others see what he wanted them to see. Once he was smoke he was able to do things like show them their lives (like Echo), ability he may have gained when he was in the light.
The people in the Dharma initiative were the ones who built Jacob’s cabin as a way of protecting themselves from the black smoke. They referred to it as Jacob’s cabin because Ben thought it was Jacob speaking to him, not MIB. Some people believe that you can protect yourselves from evil spirits by putting ash (across a doorway/in a circle like in the movie The Skeleton Key). I think that is why the ash was around the cabin. The black smoke was trapped in the cabin for a period and that is why he told Ben to kill everyone in Dharma, so he could be released. The Dharma people (who became the Others when Ben took over) obviously knew about the smoke, that’s why they had the sound poles surrounding their camp. The cabin appeared/disappeared because it was built on top of a spot with a high concentration of electromagnetism, so it flipped through time.
The island’s electromagnetic energy is what caused things to crash there (a la Bermuda Triangle). Jacob had a way of manipulating it, that’s why he kept bringing people to the island, to find a replacement/protector. The Dharma people also had found the wheel of time that the Man in Black had started and they got it to work. This wheel allowed the island to be moved to so it could be lined up with a specific point in time. This is how Jacob was able to leave the island and visit our castaways during their lives. It was also how the real Locke was able to get off the island. There was always something special about Locke, which is why he was the one who could be possessed (perhaps it was his faith in the island) by MIB. MIB couldn’t leave until he had a mortal body again.
Just like God put humans in Eden, he put humans in charge of the island. Because we are all human we can make mistakes so there were probably good guardians and bad ones. The guardians are the ones who made the ‘rules’ that is why, Hugo told Ben that they could change the way that the island was run.
The show was always about the characters and their journey/destiny as well as debate over science and faith. Jack had no faith in the beginning, so one of the main points was that he gains faith and ultimately realizes he had a destiny. All of the characters were ‘lost/broken’ in some way and they all needed to come to terms with the wrongs in their lives before they could move on. The final season’s alternate timeline was a purgatory/place that they created to help them live the lives they wanted to live, fix mistakes etc. Once they had done that they were able to move on/go to heaven/ the next world/dimension etc. I interpreted it as them going to heaven but they left it open. In The Dark Tower they were in a world that had ‘moved on’, so depending on your belief they could have moved on to another existence/world/dimension.
They all died at different points but they were all able to meet in this fictional life. They were all important to each other, their experiences on the island (and off for oceanic six) were the most important time in their lives and that is why they needed each other to move on. Jack was always afraid of dying alone (We live together or we die alone) but his father tells him that no one dies alone. This reminded me of Star Trek V when Spock tells Kirk that he shouldn’t have been afraid that he was going to die because he was ‘never alone’.
I believe that Sayid and Shannon were together because they were members of the original crash and those were the people that were all coming together. Also it was a place that they created to finish things that they hadn’t had a chance to. Sayid and Shannon never had a chance to get together because she died before him. Another reason why Shannon may have been important was that she was the one who allowed Sayid to love again. He came to the island a broken, ex-torturer, she allowed him to regain some of his humanity.
Aaron appearing at the church as a baby could also be a result of it being a place that they created (fictional) and Claire and Charlie had only seen Aaron as a baby so that’s the way that they would remember him. It could be that Aaron was able to be born on the island because he was ‘special’ like Desmond, somehow immune to the effects of time. Or there is a certain limited amount of time that the island exists in which includes the few months/weeks that it took for him to be born. Other babies could not age or come to term a full nine months.
After I had written this, I woke up and remembered that Ben and other people did age on the island (Ben grew up there). There were only certain people who were guardians (drank the “blessed” water) that were immortal, like Richard, Jacob and MIB. This means that my theory about the island being stuck in time as the reason for babies not being born is wrong. On the pre-show finale, the creators said that when Jacob touched our heroes during their lives that protected them and meant they wouldn’t die. I don’t see how that could be true because our characters could and did die. But that would be a possible explanation as to why Aaron and Claire survived his birth. As long as they were candidates, they were protected.
My other thought would be that babies couldn’t be born because of either the electromagnetism and/or the closeness to the light/source of all life. I liked my other time theory much better and was really disappointed when I remembered about Ben.
I do think that the creators had a plan and knew what they wanted the final scene to be. But I also think that in order to fill six seasons they had to come up with new mysteries all the time, so that’s why a lot of “mini-mysteries” were left unanswered.
But then I could be wrong about everything too. 
