Jacob is a guard in a sort and Smokey is the prisoner, making the island the cell. I say island because that is how the individuals who are brought there perceive it. I don’t really believe it exists in the physical world as we know it. I believe it may even exist in another dimension all together. How long this has been the case who knows. Time is irrelevant on this island as it has been said by Faraday that perceived time is different on the island as is time off the island. Every so often the guard gets a reprieve and he chooses another guard to replace him thus the candidates. The old guard resumes his life off island maybe returns to the exact instant in time that he was chosen in the first place so his/her life never really skips a beat. The candidates can be chosen from any period in time since as something about the island allows it or allows those on it to travel through both space and time all the while shielding itself from the rest of the world. Once you are chosen as the next guard you are given the rules for being the next guardian. What the crime from perpetual imprisonment isn’t known as of yet.
Over time maybe the prisoner discovered something about his prison that allowed him to swap his consciousness with the guard but with the rules of the island in place he was never able to escape only continue in the process. This is all supposition, as is this theory, so maybe the prisoner secretly found his jailer in the process of trying to locate his replacement and interfered with the process and their minds were transposed into the others body. The island maybe keyed to the guards DNA now reacts to his wishes but still locked into certain parameters that must be obeyed. The prisoner now in the form of the guard (The Jacob that we see dressed in white on the beach) tries to find a way to escape and thus started bring people onto the island. The guard trapped in the form of the MIB tells him how much he wants to kill the prisoner. He also tells him that one day he will find a loophole to his current situation.
The Jacob that we see off island may have been the guard or just as well the prisoner we don’t know yet. The circumstances of Jacobs interference could be perceived as evil in the fact that it took those who the candidates perceived as loved ones away from them. Again with the whole course correcting thing going on constantly if those things needed to be done to get a potential candidate to the island they would be most likely be undone after you were either chosen and become the next guard or not chosen and you would be placed back into your current situation none the wiser about being on the perceived island.
I say the course correcting because why didn’t Sawyer arrest Kate when they first got off the plane and saw her in handcuffs while in the elevator. I would think it a policeman’s duty to apprehend a perceived criminal. I don’t think Sawyer was a policeman at that point in time. Things changed on the island and now he is a policeman as seen in the “Recon.” As both Jacob and Flockes forces make moves on the island the fabric of time and space is molded based upon the situational outcomes on the island. I don’t think we were seeing continuity errors when Sayid’s custom paperwork changed from the time he was on the plane just before landing and the time we see it again at baggage claim. Also the gold Rolex watch face design that Jin was delivering showed that it was 180 degrees out of sync from the time he was on the plane and the instant that the customs guy inspected it.
As time goes by and more and more people are bought to the perceived island and the prisoner is bringing smarter people to the prison (aka the DHARMA initiative). They figure out ways to beat the prisons defenses. The prisoner discovers that if there is no longer a prisoner then there is no longer a need for a prison and sets in motion a plan to maybe kill the guard trapped in the prisoners’ body. Thus the look of concern on Flockes face right before he kicks the dying Jacob into the fire and he says “They’re coming.” Maybe Jacob was talking about Charles Widmore coming who appears to have the means of killing the Smoke Monster. Flocke talking to Sawyer tells him it’s either “kill or be killed and I don’t want to be killed.” Remember he also says that he has been trapped for so long that he doesn’t remember what it’s like to be free. The obvious hole in this is the fact that Miles tells Illana and the rest of the people with them that right up until he died he thought maybe Ben would or had changed. This I say that death on this island is not death as we know it and the island compensates for it somehow. So in Jacob dying on the island it wasn’t really death in our sense of the word.
The guard trapped in the prisoners body also discovers that if one of the candidates is killed he can take on his guise and replace him in the process. With this being the case he sets things in motion that makes this possible. Locke leaves the island and then Ben does also and in the process kills him. Loophole achieved for the guard and now both sides will battle it out until we see the island underwater. I say this marks the end of the prisoner who I believe will actually be the prisoner when Desmond somehow intervenes as for some reason the rules don’t apply to him. He discovers the truth about what is going on and the 6 candidates band together and undo what was done and overthrow the Smoke Monster transposing their minds back.
I also think that Locke’s dad in the alternate reality isn’t a con man. I believe that the Anthony Cooper in this reality may in fact be the Smoke monster as the woman that Sawyer was sleeping with and who they were trying to apprehend said she was married to a con man. Maybe the greatest con man of them all. He has the initials A. C. Maybe they will end up standing for the Anti-Christ the greatest con trying to be pulled on mankind yet.
This is my theory right now and it changes from week to week but the idea that who we have perceived as good and bad hasn’t waivered at all. I believe that we will find that the MIB is indeed the good guy and that Desmond will play a pivotal part in righting the wrongs that have been perpetrated on the perceived island.
When the Doctor was in his TARDIS he made a remark that stuck with me. “Diagonal thinking, that’s what’s required. Isn’t it Astra?” Diagonal = Sideways = Oblique. The hyperspace coordinates in doctor who had to be specific to 0037. When Lapidus was getting back to the freighter he had to go 40 miles N @ 305 degrees & 7 K East. 0037 can be found in these coordinates with 4 & 5 remaining. There is also a character in Doctor Who has a cylindrical thing around his neck on bigger that reminds me of the object around Dogen’s neck. While in the Shadow’s layer the Shadow is projecting holographic images of the other people with the Doctor to try and get them to go where he desires. The Doctor not realizing this at first says “You better stick with me or we’ll all get lost.” Don’t know what that means, intriguing though.
Also I just looked up one of the books (Lancelot) that was on Sawyer's dresser. I haven't read this book and don't claim to know how it ends but the summary lines up somewhat with the switched consciousness theory:
Lancelot is a novel by critically-acclaimed writer Walker Percy. Lancelot is a cuckolded man who finds himself locked up in a mental institution in the aftermath of a fire at his home, Belle Isle. Lancelot claims not to remember the circumstances that led up to his confinement until he sees an old friend, Harry, in the hallway. Lancelot shares his story with Harry a little at a time, showing the reader how Lancelot went from a mild-mannered, if bored, husband, to a murderer. Lancelot is a fascinating tale of madness that takes the reader into a world that could all too easily belong to anyone.
Lancelot welcomes Harry, the priest-psychiatrist, into his room at the mental institution, expressing confusion over whether or not he is a patient or a prisoner. Lancelot claims not to have known what.....