I've been thinking a lot about the end of season 5, when we see Jacob visiting all the people off-island. The earliest I believe is Sawyer when he is a child - followed by Kate as a child, and then the most recent might have been visiting Jack in the hospital, or Jin and Sun's wedding.
How exactly did Jacob get to these places? Let's assume for a moment he's not an all-powerful being that can project himself across the globe. Sure, he has powers, such as the ability to give gifts and live forever. But aside from that, for all we know he's just a regular human with the gift of life. The only option he has for leaving the island would be using his brother's idea - TURNING THE WHEEL.
So let's say he's getting to the end of his life, and he knows the time is coming to find a replacement. What if he actually turned the wheel and left the island for all those years, and travelled the globe just as a regular person would, to influence these candidates? What if there was a thirty year gap (however long it took him to meet everyone) where he wasn't on the island at all?
He might have assumed things on the island would be ok in his absence. He did, after all, have Richard taking care of things. But of course, the MIB had other plans. While Jacob was away, the MIB started to turn things around. Perhaps brought the Dharma people, or at least let it happen (something tells me Jacob wouldn't have wanted those scientists tampering with his light). MIB started to infiltrate Jacob's people - by manipulating Ben. Slowly grooming Ben to be the leader of the Others, thinking it was Jacob who was leading him. MIB started using Jacob's cabin. By the time Jacob returns, let's assume it's just before or around the time Oceanic 815 arrives - Jacob has spent so much time away from the island and away from his people that he becomes the more reclusive protector that he was right before he died.
Now, regarding how Jacob returned - how about this one? Christian Shephard was Jacob all along. What if MIB was lying to Jack when he said that he was Christian? Jacob could have been the first to use the trick of taking over a dead body in a wooden box. He knows the MIB could also use the body, so he takes it from the coffin after the crash and hides it. Perhaps buries it, explaining why Jack found the coffin empty. The MIB might have gotten this idea from Jacob, and then tried it himself with Locke's body. For what reason, I'm not sure.
But Jacob as Christian sure does seem to make sense, when you think about him leading Jack to water, and using the cabin. Even sending Locke off island and instructing him to bring back the Oceanic Six. We know that Jacob would want this, because he wants his candidates back. MIB then manipulated Ben into killing Locke off-island so that a nice fresh body could be returned for him too.
Or, somewhere along the lines Jacob could use his old form again, and stopped using Christian's - in this case the Christian that told Locke to turn the wheel could have indeed been MIB. And then Christian taking care of Claire? MIB.
The other hole in this theory is that I don't know how Jacob got off the island again during the Oceanic Six days, when he met Hurley and Sayid. I'd love to hear thoughts on this.
This was my first theory, and I know it has holes like most theories do. The main question I want to discuss is not the part about Christian (that idea sprouted from the main idea) - how did Jacob leave the island, and why does he seem like an absentee leader?
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