SOBEK Inhabits Jacob & SET inhabits MIB
Ok, my theory is sketchy, and doesn’t answer everything, but for what it’s worth, here it is. But first of all, let me say that people’s attempts to draw Christian/Judaic parallels from this show, are wasting their time. Originally I thought there may have been a link, but after this season, I am sure there is nothing remotely relating to Christianity. Jason is not God, and the MIB is not Satan.
Remember that in Christianity, God is a triune God (Father, Son, and Holy Spirit), and Satan is nothing more than a fallen angel, even though he inhabits the serpent in the garden of Eden to tempt Eve. Likewise, the island is not the garden of Eden. Did you ever see a tree of knowledge of good/evil, or a tree of life on the island of Lost?
In the Lost series, I think that the Spirits of the Egyptian Demon/Deity(s) SOBEK & SET inhabit the bodies of Jacob & the Man In Black (MIB). Think of them kinda like Ying/Yang – but even that’s probably not the best analogy.
Jacob and MIB probably first came to island many years ago and were inhabited by these Demon/Deities. MIB/Set is tired of the stagnation of the never-ending struggle and is trying to make it change. He is looking for a loop hole to end it all, regardless of the outcome. Jacob/Set is remaining true to the way it’s always been – keep to the old ways.
Jacob = Sobek
See http://en.wikipedia.org/wiki/Sobek and http://www.fruitofthenile.com/sobek.htm for info on Sobek. Sobek was a repairer of the evil which Set had done. Sobek brings together elements that has been separated by evil. The Egyptian Book of the Dead cites Sobek’s assistance of the deceased. He restores the deceased’s eyes and mouth, protects him/her from Set and leads them to heaven.
MIB = Set
See http://en.wikipedia.org/wiki/Set_(mythology) and http://www.fruitofthenile.com/set.htm for info on SET. He instigates change where things have grown stagnant, whether it be for good or evil. The distinction is irrelevant to him. In this sense he brings about new beginnings, even if they should arrive unwelcomely. For this reason, he is a demon-deity of change, confusion and chaos. Also, anyone who has read any of the Conan books, knows that Set is depicted as Snake-like.
For this reason, I suspect the smoke monster (which is somewhat snake-like) comes from Set, who is pronouncing judgment on whoever it comes in contact with. Remember it judged Mr. Echo. Also Ben went to the smoke monster temple (with the false John Locke impersonated by MIB/Set) to be judged. This explains why Ben was told to do whatever false John Locke said. When the real John Locke first encountered the smoke-monster, he was judged to be useful to Set and didn’t get killed. However the real John was told by Christian he’d have to die in order to bring back the Oceanic 6. This makes me think that Christian was impersonated by MIB/Set also.
So in the season finale, MIB sees the ship, and there is some question of whether the ship is leaving or coming, but I think it was coming, and I’m guessing Richard Alpert was on it. MIB asks why Jacob brought the ship to the island — is he still trying to prove MIB wrong? MIB says they come, fight, destroy, corrupt, and it always ends the same. Jacob tells him it only ends once, and everything else is just… progress. MIB says he wants to kill Jacob, and one day he’s going to find a loophole. The Man in White says he’ll be right there.
So the big question for me is: does Ben’s knifing of Jacob in the present get undone by Jack’s setting of the hydrogen bomb in 1977? Wouldn’t all the ‘others’ (a.k. followers of Jacob/Sobek) be completely annihilated? Or does the fact that it’s only the plutonium core, make it so the Others don’t die…maybe Jacob/Sobek saves them somehow? After all, he probably needs those worshippers. Also, maybe there’s other demon/deities on the island as well. Maybe Osiris & Isis are inhabiting Bernard and Rose for all we know. Hmmm…it’s a dilemma which could go any direction…all of which I suspect will have loopholes in the explaining of all the minor details.
Like I said, my theory is sketchy.

Elvis_Is_Dead, I like your theory, but don’t know if the smoke monster and Jacob’s Nemesis, are one in the same.
I wouldn’t even be so certain, if we know which one of the two is good or evil. I think that is debatable at this point, as there are arguments on both sides.
I am thinking that ‘the losties’ and the outcome of ‘the incident’, may not make a difference in Fake Locke’s killing of Jacob. At least in terms of changing it.
I have some other thoughts on that!
Good thoughts!
I m with dabs, I think Jacob could still end up being the bad guy. The only thing which makes me question this is. I would not expect “the good guy” to say I am going to kill you. I firmly believe Jacob touched many of the l;osties because he knew what was going to happen. (until the end everything is just progress) I think this statement may be reference to history repeating. Jacob knows he is to die and now has a failsafe of his own in the losties who will now come back form the past to fight for him. Its just the why i dont know. They don’t know Jacob. Could the losties lie in the shadow of the statue “He who will save us all” That will bring around many of our main charcters redemption I think. SAyid, KAte, JAmes, JAck are inherently good people who have done bad things due to circumstamce Jacob will prove them right. I believe this next series despite my initial real concerns about not finidng things out can be a stormer. The ultimate battle good v evil is always fun..right???
Maybe he touched them to somehow mark them. BTW: Couldn’t Sobek/Set be MIB/Jacob just as well. I like this theory ‘cuz I was lookin’ at these two earlier when I though Juliette was that crazy fertility goddess.
I don’t know if anyone has said that the story or characters on the show directly relate or actaully are stories and characters from Christianity. I think you’re right, saying that would be a waste of time. For the same reasons saying that the story and/or characters are actually going to be stories/characters from Egyptian Mythology is a waste of time.
There are parallels to both, obviously. But Jacob and his buddy aren’t God and Satan. They’re not Cain and Abel. They’re not Sobek and Set either.