The Loophole by CMR

This theory attempts to put the MiB's plan into context and explain how Jacob ended up thwarting him. But first, we need to sort out and revisit several things.

1. Time Travel

In the canon of the show, "whatever happened, happened". (But not necessarily with Desmond, however that's not important here) Everything the Losties did in the past had always happened the way it did.

What we don't know about time travel is how the flashes during season 5 worked. Why did only the Losties time travel and not the Others? Why did they end up in the time periods that they did? Some propose that it was the island's will, some say random time jumps. My proposition: The time jumps were being controlled by the Man in Black.

Before I explain why that makes sense, let's discuss one (of perhaps many) looming inconsistency. When John Locke went down the well in 'This Place is Death' he shouldn't have found the donkey wheel off its axis. Ben turned the wheel in 2004 and Sawyer & co. found themselves pre-1867 at that point. One possible explanation? Think of the wheel and the immediate area around it as a time machine. Much like the DeLorean in 'Back to the Future', it is the means by which people can travel through time and it travels with them (although in this case you don't actually have to be IN the time machine). You'll have to suspend disbelief for a moment and allow for the idea that two objects can occupy the same space if you were to believe this theory, but we've believed more spectacular things.

Now, if the donkey wheel is the time machine, who is the driver? The Man in Black, of course. And we have evidence that he was time traveling with the Losties as well, as he should not have been in the guise of Christian Shephard in the time period he was in. So it is my belief that he was down in that well controlling these flashes all along. How, exactly? There is no real answer, but there is enough information in the show to lead us to believe that it would be possible. For one, we know the Smoke Monster was born from the light in the heart of the island, a similar light to the one found in the well, so we can assume there is at least some connection there. We also know that the MiB planned to manipulate that light to leave the island at one time, and also that he has a gift that allows him to understand how things work intuitively (both revealed in 'Across the Sea'). While nothing is concrete, there is enough information there to fill in some blanks.

2. The MiB's plan

It is somewhat commonly believed that the MiB's plan was to take John Locke's form, get Ben to kill Jacob and then kill the remaining candidates. My theory argues that in fact his plan was to first kill the candidates, then take Locke's form and have Jacob killed. And he thought he accomplished this in the season 5 finale, but we'll come back to this.

3. The Compass

The one Richard gave to Locke, and Locke gave to Richard in an endless circle? It's not important, but the concept is for the Man in Black's master plan.

Now that we have that out of the way, let's discuss what the Man in Black's plan really involved.

Pick up in 2004, Ben had just turned the wheel and sent the island on a wacky journey through time (being controlled by the MiB, as previously discussed). First important destination: 1954. Dropping the Losties off there allowed for Locke to set himself up as future leader of the Others, which was important as the MiB would need to take the form of somebody with authority in their ranks. Again, this was like the compass. Locke thought he was destined to become the leader of the Others because he told them in the past, which led them to think he was important, which led him to believe he was, etc.

Next important stop: pre-1867. Things get a little muddy here, but this is the most important stop in their journey. What we know about this time period is that the statue has been erected and that the well has apparently not been dug yet. The easiest explanation (though not one that I necessarily subscribe to) is that this takes place between the time when the MiB leaves Jacob and Mother and the time when he becomes the Smoke Monster. Let's call it year X.

What happens next can either be very simple or very complicated, but the result is the same. The simple explanation is that the rope Sawyer leaves in the ground is found by the Man in Black's people and is used to discover the well, thus setting off the chain of events that would lead up to the year 2004 and Ben turning the wheel. The complicated one involves believing that the MiB from 2004 (as Christian Shephard) visited his past self and filled him in on all that he'd need to know until 2004 in order to execute his master plan.

Either way, a time loop is created similar to the one the compass is stuck in. There is no starting or end point to the MiB's plan, and thus it cannot be stopped. Everything between year X and 2004 has to happen because "whatever happened, happened", and thus Jacob is helpless to stop it (presumably). This is the "loophole" that the Man in Black found, a literal loop in time that prevents Jacob from stopping him.

Back to the time travel and the final stop: 1974. He deposits the Losties there because he knows because of his 2004 knowledge (or thinks he knows) that 3 years later the rest of the Candidates would wind up in 1977 and eventually kill themselves by detonating a hydrogen bomb at the site of the Swan. Thus, when he returns to his rightful time, all the Candidates will be dead and all that would be left would be to kill Jacob. This would explain his surprise at Jacob's revelation in 'The Incident' that "they're coming." He thought he was done, that it was over, and this kink in his plan infuriated him.

But how did Jacob know they were coming? Because he brought them. Much like the Man in Black, Jacob could manipulate time flashes himself. When Ajira 316 came back to the island, he flashed the Candidates off of it (assume he only needed one Kwon, and he already had Jin in 1974). He knew that the Candidates would be safe in 1977 because the Man in Black thought they were destined to die. Then, when Jughead detonated, another flash orchestrated by Jacob brought them all back to 2007, safe and sound (for the most part).

Thus, Jacob used the MiB's own plan against him. Season 6 was essentially the MiB scrambling to finish what he thought he had already done.