Desmond is Dharma's Candidate, Dharma is the antagonist by CruzaderJC

I believe the battle isn't between Jacob and the Man in Black. The MIB is just a disgruntled part of the game who doesn't want to play anymore, so he sets up Jacob's death so he can leave. I believe the opposing force to Jacob will be Dharma trying to reestablish itself back on the Island. Thus, Jacob is trying to protect the Island from THEM. Jacob vs. Dharma. Faith vs. Science, just like the show has ALWAYS been.

Sawyer asks, "What are we protecting the Island from?". Flocke answers, "From nothing, that's the joke, to protect the Island from nothing."

Sound familiar? Desmond was told to press the button in the hatch every 108 minutes. Why? To keep the world from ending. Did he do his job? Yes. For a very long time.

Methinks the Dharma Initiative caught on to the game and tried to establish its own trial for Candidacy. They BROUGHT people to the Island. Desmond may have been in the Hatch solely to prove he would be the Dharma's Candidate for the island.

Faith vs. Science? Jacob has his candidate and Dharma has their own? Maybe, but all I know is that the concept of the 108 minute Hatch has always been an integral part of the story and will come back into play, just like Desmond.

Here's a thought... what if Desmond is ALREADY the Jacob-like character in the ALT Universe? Might explain why he seemingly disappeared on the plane...