This is my theory that I already posted on a Facebook forum:
First of all, let's talk about Jacob and Man #2. I believe they are two different gods, set at odds with one another. Not really good and evil, but two different gods with separate goals. Jacob has the ability to heal, has some awareness of the future, and can influence people to bring them to the island. Man #2 has the ability to take the form of anyone who's dead body is somewhere on the island. This is how he manipulates people. He also resents Jacob's manipulations which bring people to the island. Every time we saw someone who was already dead appear to someone on the island, it was the Man #2 at work. This includes all of Christian Shephard's appearances on the island.
My theory is that Locke never saw Jacob in the cabin. The cabin used to be a safe place for Jacob to use to communicate with his chosen leader without revealing his primary residence in the statue. However, the protection placed on the cabin was lost (as evidenced by Illana's reaction to the ash-line being broken) and Man #2, the Ghost-god entitiy, had taken over the cabin. Locke was being constantly manipulated by this second god when he always thought it was Jacob. That means Locke was never the leader. It was always Ben. That's the loophole. Ben was able to go in to see Jacob and was able to kill him because he had never been dethroned as leader. (By what Richard said, "Only the leader can request an audience with Jacob", i think it implies that only the leader can kill Jacob)
Jacob saving Locke after his fall from the building tells us that Jacob always intended Locke to be on the island. The flashbacks with Jacob and the Losties shows some of the little and big influences he had on them all that led them to the island. However, Locke and the Ghost-god created the sense in Richard that Locke was destined to be the leader. Richard had met Locke in the 50's and always thought Locke would one day be the leader since then. However, Locke was always getting his orders from the Ghost-god. His purpose was to lead Ben astray. He was the ultimate Red-Herring, both when alive and when dead. This plays into the symbolism of the fish Jacob catches at the beginning of this last episode.
Also, I think the only reason that Jack, Sayid, Kate, and Hurley went back 30 years was Man # 2's attempt to get them out of the way. They were the only one's that knew that Locke was dead and that his body was on Ajira 316. (Except for Ben)
Look at who stayed in present time:
Lapidus - Never knew Jeremy Bentham, didn't know he was dead, never saw the cargo
Sun - Locke never visited her as Bentham, so she didn't know of the alias or his death. (When she saw Locke's real body she asked "Then who was that?")
Ben - He needed to be in present time because he was the main pawn of Man #2. The only reason that seeing Locke alive didn't raise a flag was because Ben thought he was already special and, more so, the leader of the others.
Also, Ben being the only one that knew Locke was dead on Present-Island kept him from having corroboration with a claim that Locke was dead. And Ben didn't rush to admit that he was dead anyway, seeing as how he killed him.
So on my third time watching the finale I also noticed at around thirteen minutes (with commercials):
John Locke says,
"...Once I've done that, we're going to need to deal with the rest of the passengers from the Ajira flight that brought me here"
Alpert: "What do you mean 'deal with them'. "
Locke: "You know what I mean."
Since we know now that Locke is Man #2, I think this implies that he knew that Illana and Co. were all working for Jacob and that he wanted to get them out of the way is quickly as possible.
First of all, let's talk about Jacob and Man #2. I believe they are two different gods, set at odds with one another. Not really good and evil, but two different gods with separate goals. Jacob has the ability to heal, has some awareness of the future, and can influence people to bring them to the island. Man #2 has the ability to take the form of anyone who's dead body is somewhere on the island. This is how he manipulates people. He also resents Jacob's manipulations which bring people to the island. Every time we saw someone who was already dead appear to someone on the island, it was the Man #2 at work. This includes all of Christian Shephard's appearances on the island.
My theory is that Locke never saw Jacob in the cabin. The cabin used to be a safe place for Jacob to use to communicate with his chosen leader without revealing his primary residence in the statue. However, the protection placed on the cabin was lost (as evidenced by Illana's reaction to the ash-line being broken) and Man #2, the Ghost-god entitiy, had taken over the cabin. Locke was being constantly manipulated by this second god when he always thought it was Jacob. That means Locke was never the leader. It was always Ben. That's the loophole. Ben was able to go in to see Jacob and was able to kill him because he had never been dethroned as leader. (By what Richard said, "Only the leader can request an audience with Jacob", i think it implies that only the leader can kill Jacob)
Jacob saving Locke after his fall from the building tells us that Jacob always intended Locke to be on the island. The flashbacks with Jacob and the Losties shows some of the little and big influences he had on them all that led them to the island. However, Locke and the Ghost-god created the sense in Richard that Locke was destined to be the leader. Richard had met Locke in the 50's and always thought Locke would one day be the leader since then. However, Locke was always getting his orders from the Ghost-god. His purpose was to lead Ben astray. He was the ultimate Red-Herring, both when alive and when dead. This plays into the symbolism of the fish Jacob catches at the beginning of this last episode.
Also, I think the only reason that Jack, Sayid, Kate, and Hurley went back 30 years was Man # 2's attempt to get them out of the way. They were the only one's that knew that Locke was dead and that his body was on Ajira 316. (Except for Ben)
Look at who stayed in present time:
Lapidus - Never knew Jeremy Bentham, didn't know he was dead, never saw the cargo
Sun - Locke never visited her as Bentham, so she didn't know of the alias or his death. (When she saw Locke's real body she asked "Then who was that?")
Ben - He needed to be in present time because he was the main pawn of Man #2. The only reason that seeing Locke alive didn't raise a flag was because Ben thought he was already special and, more so, the leader of the others.
Also, Ben being the only one that knew Locke was dead on Present-Island kept him from having corroboration with a claim that Locke was dead. And Ben didn't rush to admit that he was dead anyway, seeing as how he killed him.
So on my third time watching the finale I also noticed at around thirteen minutes (with commercials):
John Locke says,
"...Once I've done that, we're going to need to deal with the rest of the passengers from the Ajira flight that brought me here"
Alpert: "What do you mean 'deal with them'. "
Locke: "You know what I mean."
Since we know now that Locke is Man #2, I think this implies that he knew that Illana and Co. were all working for Jacob and that he wanted to get them out of the way is quickly as possible.
