In this theory I will use my gut only..and some evidence provided by the show.
I believe neither Jacob or MiB are good/bad. Its their goal that defines them. Similar to Jack and John. Both good men but with entirely different perspective. One believes (John) that the island is a place where miracles happen and that the best thing to do is to just let it be and stay on the island..live and protect it. The other one (Jack) doesn't believe in miracles even thou he saw his dead father walking around.
He also believes this place is just an island and it doesnt need protection. The survivors should find their way of and leave this place. Never to look back.
Which one of these two is right? Probably both. It depends on others around them.
I choose to side with John, since I am a spiritual person and I believe in miracles especially if one happened to me. I also side with John because now I know he was right..he was always right, from day one.
This leads me to two men, again. One is John and the other is Desmond.
I believe both men have seen the future/past. The only difference is we know about one, Desmond (via "Flashes before your eyes")..I always wondered what happened to Locke after the hatch imploded.
We know that Des was so close to the epicenter so his life literally flashed before his eyes. But what happened to Locke and Eko? Eko started having visions of his brother Yemi. And these vision eventually lured him towards his death. But Locke woke up about the same time Desmond "came back from London", and he was mute. At the time I thought it was island who wanted him to shut up and listen but now I think something else happened instead. (or both)
I believe Locke lived/felt his future. The strangulation. First thing he did when he woke up he grabbed his neck. He felt something is wrong. So my guess is that he psychologically experienced strangulation..by Ben in the future. If that is even possible..
I have speculated number of times so far about Locke being able to see the future. But he misunderstood this by talking to an island. And we have seen things through his eyes..I asked Ricky when was the first time Locke started "talking to the island" and Ricky told me it was right from the start, since "Walkabout".
It could be two things:
1. Locke is able to see the future
2. Locke is having deja vu, meaning he already lived this life and started to remember..feel what is gonna happen next.
I cannot separate these two things. Because I am still not sure if this is a loop what we are witnessing. But the possibility of reincarnation is real deal. The question is whose spirit is implanted in Lockes body (starting with the young age when he drew a smoke monster)
But one way or another it is undeniable fact that his dreams are not dreams..they are glimpses of the future. Desmond is having them in normal state of his body and mind via flashes, Locke is having them in his dreamlike state, via dreams.
The best example is an beachcraft dream. In that dream he saw both, plane crashing (which happened few short months after in the past/Lockes future) and Boone dying (which happened few days later)..Theresa falls down the stairs was just a hint, but we misinterpreted it. Boone told him that-in the future, right?
My only goal (by writing this theory) is to present you my doubts and thoughts..and ask you your opinion..or correction if I am mistaken.
Lets continue. Episode "Live together, die alone" has certain dialogues worth of reviewing again. Especially one between Locke and Desmond. I will give you my opinion about a certain dialogue.
Desmond: What if you got it backwards?
Locke: Backwards?
Desmond: What if the experiment wasn't on two men in here but two men in there?
The key words are: TWO MEN, EXPERIMENT, BACKWARDS.
We always have two men: Jacob/MiB, Ben/Charles, John/Jack..two men in Pearl, two men in Swan..two men killing Cooper/Two men killing Jacob (both times one man is Locke manipulating other man into killing)..is that a coincidence? I doubt.
Experiment is successful in one case..if it has an observer. So someone needs to observe something evolving, otherwise nothing happened, right?
Backwards is an interesting choice of words. Since everything we are seeing is sort of backwards. We were first shown the consequence then the cause.
A lot of people speculated that Jacob is someone we know (Aaron perhaps) who is jumping from the future to various periods of time in past. But what if it is Jacob who saw the glimpse of future and now is doing everything possible to make sure the "end" comes.
Jacob: It always ends once. Anything that happens in between is just progress.
What is the end he is talking about? What is the progress?
I believe the end he mentioned is the end of the world (and that is what he saw). When I put two and two together this is the only thing logical to me. Why? Because of these things: Valenzetti equation that predicts the end of the world, the numbers, the upcoming war, "God help us all" and so on.
The progress he is talking about is the progress towards the end. The variables in this equation are the people. We talked about it..the past cannot be changed. But future could, because future hasn't happen yet. So Jacob is using people, manipulating the events progressing towards the end. MiB wants to be left alone. The only thing he cares about is his island.
Like Carol Ann said (if I recall correct), the worst people Jacob brought to the island are soldiers who decided to test the hydrogen bomb on this beautiful place.
Jacob fails each time (thus the need for "proving MiB wrong" because so far the MiB is right)..so the only possible way for him is to create a loop, start over and eventually bring the end. "They are coming" means he found the way to prolong events, maintaining the loop.
There is another way to look at things. The war is about the timeline. The ruler of one timeline is Jacob. The ruler of another one is MiB. But I don't see this happening because we are left with one more season. 18 episodes to go.
However there is a different time line. And these timelines somehow crosses paths on this island. Weather the island just is..or it is created by both scientist and military working together (because both US Military and DI scientist knew about the island and looked for it. Looking for something means you are aware of its existence, right? So I am asking you how did they know about the island? The Hanso journal is not possible Ricky-it was clear that none looked inside until Widmore got it, unless it was yet another lie) it stays open.
This is something we talked about and I put it in a theory. We will continue from here giving our possible ways of unfolding certain things.
Thanks for reading.