In the pivot final scene of S5, Flocke (Fake Locke or Dead Locke) is recognized by Jacob as the MIB from the beach scene. Flocke acknowledges that he (MIB) had found the loophole to kill Jacob. The only motivation we know of is that MIB did not want Jacob to continually bring human (souls) to the Island. All they do, MIB insisted, was fight, kill and make a mess of things. This is the Conflict. The loophole the apparent solution to the Conflict.
Some comments on the relationship between Jacob and MIB. Both are apparently equals in some regard. They must have equal status or equal powers on or through the Island. The balance of power may be as simple as one controlling above ground and the other controlling above ground. They cannot directly kill each other, otherwise MIB would have killed Jacob on the beach. However, one can apparently get a human soul to do the evil deed under the right circumstances (the loophole).
Since we are fairly certain that MIB can manifest himself as Smokey, there is an open question on how Jacob can manifest himself.
It may get down to contact or touch.
We have seen Jacob "touch" the following characters: Sawyer, Kate, Jack, Jin, Sun, Locke, Ilana, Sayid and Hurley. All those contacts occurred off-island in public places.
We have seen MIB, as Smokey, have contact with the following characters: Seth the Pilot, Locke, Eko, Kate (scanned), Juliet (scanned), Nikki & Paulo (spiders), Ben (as shot boy taken to the underground chamber), and Alpert (? who took Ben into the underground chamber).
We can also suspect that since MIB is Flocke, that he can reincarnate the Dead who arrive on the Island: Christian and Locke. We have also seen MIB ghost in contact with Claire and Aaron (though Christian).
When we compare the Lists, we find that only one character was physically touched by both Jacob and MIB: Locke. And the tipping point in MIB's favor was bringing Dead Locke to the Island so MIB could reincarnate into Flocke, to lead follower Ben into a treasonous rage which results in Ben killing Jacob (the loophole) for MIB.
It may be a simple as a game of tag: with MIB "tagging" Locke twice to Jacob's once in so far as MIB creating and controlling Flocke in the end.