There are a lot of theories out there about who or what Jacob and the Man in Black really are.  Here's some of the more popular theories out there:

1.  They are gods or demi-gods (Egyptian, Greek, etc.).  The island mythology is chock full of hieroglyphics and ancient looking architecture.  Jacob and MIB could be playing a game that decides the fate of the world and people throughout history have been their playing pieces.  There is a scene in season one where Locke is telling Walt all about backgammon.  He explains it's a game older than Christ, there are two sides, one is light, one is dark.  Throughout the run of the series, Ben and other characters have stated they are the "good guys".  In season five, Bram is trying to talk Miles into joining his team and not Widmore's.  He tells Miles that there is a war and Bram's side is "the winning side".  MIB is looking for a loophole so he can kill Jacob.   Jacob visits certain characters off-island and gives them a slight touch.  After Ben stabs Jacob, Jacob tells MIB (disguised as Locke) that they are coming.  Did these touches change the game pieces in a way that counteracted MIB's moves?

2.  They are scientists from the future.  Something very bad (Earth's destruction?) happens in the future.  Jacob and MIB were sent back to an island known to have special properties.  They have extensive files on each of the characters and the events in their lives that are changable.  They give instructions to certain players (Ben, Eloise Hawking) so that they can influence characters to make different choices in the timeline.  Once on the island, they become immortal, and are tasked with bringing certain people to the island until the right result is achieved and the timeline is fixed and crisis averted.  The plots get rebooted at the point in the timeline where it went off-track.  MIB has seen the same scenario so many times that he has become jaded.  He wants to kill Jacob and stop the crazy loop forever.  Jacob sees progress, little by little, towards the desired result.

3.  Free Will Advocate versus Fate Advocate.  The free will and fate discussion has popped up constantly on Lost.  The beach conversation between Jacob and MIB seems to be about this as well with Jacob in the free will corner and MIB in the fate corner.  MIB believes people are destined to make the same choices again and again and desperate to stop the endless cycle.  Desperate enough to kill Jacob.  Jacob believes people should be given choices, and gently coerced into making the correct decision.  We have seen Ben consistently use this method.  For example, when Ben had a tumor and needed an operation, they could have forced Jack to do the operation.  However, Ben says "I want you to want to do the operation".  MIB is using Locke's need to feel special to play the fate card, while Jacob is slowly trying to change the outcome one reboot at a time.

What's Your Theory?

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