THERE IS ONLY ONE TIMELINE
In episode LA X we are introduced to a different chain of events than what we saw in the seasons prior to The Incident. I think we are being led to believe that this is some sort of parallel or alternate time line. However, my theory is that there is only one time line. That when the Jack and Co. detonate the H-Bomb they create a new future and forever change their present. Also this theory deals with the apparent inmortality of Richard and what is the smoke monster. It is not an attempt to explain all the science behind what is happening. Rather I'm looking at this from a time travel similar to say Back to the Future.
THE RULES
I'm gong to make some time travel assumptions and back them up with examples. When you travel back in time you don't age until you catch up to your time (this is from several other theories not mine). But I'm going to add that you also can't be killed if you are important to a future event. In a way you are a character in some one elses book. You appear to have choices as you develop, but in fact some one already wrote the end. However, the author of this book is also a character in some one elses book etc.
Let's look at the most relevant example, Richard. He doesn't age, and can't die or kill himself, but in episode "Dr. Linus" he tells Jack that he can do it. This is true because Jack is ahead of Richard in the time travel line. Had Jack walked away he would have succeeded. But because he stayed, it would have been Jack's suicide, and because he is meant to do something important (in other words its already happened from some one else perspective) the fate/time line has a funny way of avoiding the explosion. Also note that Richard had to give Jack permission to kill him. If he hadn't, it would have made Jack an assasin, and for what he needs to do his "balance" can't be tipped to the dark side. This example also assumes that Richard is from a time traveler and Jack is ahead or at par with him.
Another example, the others and the 815 survivors. For all the bad things the "others" did and all the people they appear to have killed something can easily be missed. They never killed anyone from 815 instead it was always the survivors who killed the "others". Let me explain, they captured, held at gun point, threatened, played mind games but who did they kill? Sun kills a girl on the boat (who by the way didn't think Sun would or could do it). Charlie kills Ethan. Ethan failed to kill Charlie when he tried to hang him from a tree. That is because Ethan is behind Charlie in the timeline and Charlie was meant to do something important on the underwater station. An event that had to happen. Another example, Michael kills Analucia and Libby. The others force him to do it because they can't kill them themselves.
The "others" have always been at a disadvantage in the time line. It gave them special abilities and a resistance to sickness and even death. They maintained the island in a state of suspension in time due to the numbers every 108 minutes. In a way they were permanently in the past say in 1985 for sake of argument. But for this reason, no one could have a baby in the island after the hatch and the 108 minutes device was built. Because how can a new life come to exists while time traveling. So course correction, the mother dies before she is able to five birth. Why? because the rule is the new life starts when she gives birth. Before that for 9 months she is able to carry it because it is a part of her. Please don't flame me for this it is not my personal view on life just the way I think the story telling in the show explains what a new life is.
The "others" are always protective of new comers to the island, because, they are new. Anyone who comes after them would be ahead of their time. So with Dharma they had a truce. When it looked like they were becoming a threat they kill them. Wrong, they can't kill them directly so they use Ben who is from the same time as Dharma to gas everyone.
TIME DOUBLES
If you followed this so far, let's consider what happened in the "LA X" episode. We see a plane that never crashes in a sideways flash and the group from 1977 coming back to the island. Two time lines? I don't think so. I believe that what hapened is that they permanently changed events and their present. They are in a time machine or buble which is the island. If they were to take a boat off the island they would realize that the world is some what different than what they left behind.
During a conversation in 1977, Sawyer tells Jack that he could have left the island and stopped the con-man from causing the death of his parents, but chose to leave things be. So that also means that there was a young boy "James" who he could have gone up to and talked to etc. So, according to this time travel can create two of you at the same time. This young boy is the one we see on the plane that never crashes in "LA X".
Another example, Dogen is promised by Jacob that his son will be saved if he comes to the island and accepts this new job. What this means is that Jacob brings Dogen to the island (the time buble) and changes the event that causes the car accident that kills his son. But Dogen can never see his son again. Why? because in changing the event, Jacob created two of Dogen. One on the island, and the other who is raising the boy. Probably Jacob has two reasons for this. One he needs people on the Island who are loyal to him, and also he is somewhat playing God. He pick people who have a sin to pay for and makes their lives better. But as payment he owns their lives on the island.
Evil Locke does something similar. He promises Sayid he can have Nadia again, because he knows and so do we that she is alive as a result of the new events in time. But again, there is another Sayid outside the island. Evil Locke is trying to do the exact opposite of Jacob. He plans on replacing the nicer version of the "6 Candidates" off the island with the dark version of the same people. This will give him an army of loyals off the island where he has a plan to do something big.
TIME TRAVELING BUNNIES
So that is why they are not supposed to leave. There are other versions of some people out there that would prevent you from going back to your life. When people have left the island they use fake ids and names. But I think there is more to this. Remember Dr. Kendal and the experiment with the time traveling bunnies. They both had a number 8 on their side. I think for them to say "don't let them touch each other" means that something bad happens. Perhaps in an earlier attempt, say bunny number 4 (Locke's number by the way) the bunny touched its time double.
Thanks to Lyn's dad for pointing out the Pauli exclusion principle which, really simply put, sais no two particles can occupy the same time and space. This idea has been used in many movies and books to explain the dangers of interacting with yourself in the past.
So, what if this is the smoke monster. What if Locke is one of the people who actually touched and interacted with himself during the time travel. What if the smoke is a collection of all the people in the island who have "POOFd" Perhaps what happens is that the time double who is ahead of the other stays and the other one poofs. Maybe that is why we see locke as a body and some times as smoke. They are separate but linked together.
Maybe, this could also explain the ash circles. The smoke monster can't cross because it is the ash of dead people. People who have time doubles as part of the smoke monster, which if it touches would create an "anti-POOF"?
LOCKE HAD TO KILL HIS FATHER
Locke needed to be able to walk in order to complete his mission. Ben shows Locke his father on the island telling him that he has to kill him. I believe that Locke from future is telling Richard to tell Ben to say this. This is like when he tells him to give the compass to himself. Lockes father remembers the con he did to Sawyer, but he doesn't remember pushing Locke out of a window. Probably, if he was telling the truth, that means that Lock's dad was pulled from a time before the event that paralyses Locke. So the event never happens. But then why is Locke still in a wheelchair in episode "LA X"? I don't have an answer but perhaps he could be in the chair for a completely different reason. In the following episode Locke's fiance says they should invite his father to the wedding. So something is very different this time around. Probably for reasons similar to not being able to kill yourself, you can't kill your father while you time travel. So Sawyer had to do! it for him
CHRISTIAN SHEPHARD
I think that Christian Shepherd on the island is a time double. Perhaps he was brought to the island by Jacob and given a job similar to Dogen. Maybe he felt responsible for the things he did to Jack when he was young and he is given another chance. I think the name Shephard on the lighthouse actually refers to Christian and not Jack. On the mirrors Jack sees the image of the house he grew up in. But Jacob came to see him at a hospital not his old house. So perhaps the house was where Jacob visited Christian.
WHY JACOB DIES
The reason is the loop hole of course. As my theory so far explains, anyone ahead of you in the time line has the upper hand on you when you time travel. Jacob had the ultimate power on the island because he was ahead of everyone else in time. Lets say that his time is 2008. He was even ahead of the 815 survivors who got to the island. But when they left the island even though they weren't supposed to and later came back they leapfroged Jacob. Now none of the 6 candidates could kill Jacob because they play a part in Jacobs story. So you needed someone else to kill him. Ben sneaks out of the island when he finds out that Locke was going to bring the people back. He realises that it is a two way trip. Normally, you leave you don't come back. So Ben usurps Locke's exit and in a way he is a stowaway on Ajira. When he comes back it is present time. He has lived some time off the island in the year 2008. So when he comes back to the island he is able to kill Jacob be! cause the are no longer in different times. The clue to this is what Myles says in episode "Dr. Linus". He tells Ben that up to the last second before he dies Jacob is hoping that Ben will do the right thing. That means that Jacob doesn't know what will happen next so he is in his present and not time traveling. So he is vulnerable and can be killed. But before his death he puts a plan together.
HOW DO YOU LEAVE THE ISLAND?
Evil Locke tells Sawyer that they need to leave the island together. I think that he is talking about something similar to what Richard asked Jack to do for him. During an episode where Hurley is talking to his imaginary friend Dave, he is told that the way to leave the island is to jump off the side of the cliff. Maybe that is how they exit. Maybe when you die you are joined back with your time double and you become one again.
But you can't just kill yourself. Because if you are time traveling and you killed yourself, you would cease to exist thus undoing your murder which would bring you back into existence where you would travel back in time to kill your self, creating a paradox. So someone else has to do it. So Locke has a plan where they do this together and don't break the rules. It sound dark, but so was detonating an H-Bomb to fix things.
WHY CAN'T LOCKE BE KILLED?
I think we are being misled by the show into thinking that Locke is a superhuman. I think that accordign to the rules in this theory, all six candidates are indestructible because of the mission they need to complete. The end has been written including them, so nothing can kill them. That is why Jack doesn't explode with the dynamite, Sayid doesn't drown, Locke doesn't die from the knife, Jin didn't die in the freighter when it exploded.
JACOB'S PLAN
I believe someone has touched on this but here is my version. Evil Lock's plan was to infiltrate the others passing himself as a good man with a rightfull claim to be leader. He gained confidence so he could get close to Jacob. Jacob also has a plan up his sleeve. I belive it is exactly the opposite. Where Lock was a bad man disguised as a good one, Sayid is a good man who appears to be bad. Remember that Jacob asks Iliana for a favor and she ends up bringing sayid as a prissoner. Perhaps Jacob trusts that Sayid will get close enough to Locke to be able gain his trust. But when he must make the final decision, the good in him will prevail.