MAN IN BLACK: Do you have any idea how badly I wanna kill you?
The motive of The Man in Black is to leave The Island. But The Rules prevents him from doing so. Jacob and his followers believe that The Man in Black is evil incarnate,hence has to be trapped on The Island. Once The Man in Black realized that Jacob's rules wouldnt let him leave,he began looking for a loophole to be able to leave the island.This includes manipulating some one not bound by The Rules to kill Jacob. Richard Alpert is the first known attempt of The Man in Black to find his loophole.But Jacob was able to successfully defeat him.
The Man in Black accomplished his loophole by manipulating Ben to kill Jacob. Moments after The Man in Black and Ben entered the Statue chamber,Jacob stated that The Man in Black had found his loopshole.
JACOB: Well, you found your loophole.
And it became an apparent that Jacob did not want to defend him self.
Many survivors of Oceanic 815 and inhabitants of The Island were manipulated by The Man in Black in attempt to find his loophole,such as Ben and Locke.The Man in Black would often use his shape shifting abilities to get this done.