Whilst I don't go with the theories that the Island is a literal cork, keeping all the evils in some sort of prison under the sea, BUT: what if the Island is similar to Pandora's Box from Greek mytholgy? If you don't know, Pandora was given a box by the Gods, but was told to never open it, as she would unleash all the evils on the world. However, she did, and, as the Gods said, all the evils escaped it and spread around the world, HOWEVER, she managed to shut it in time to keep one last thing in: Hope (considered to be the worst evil).
Maybe there is some sort of Hope on the Island, just one that could kill MIB or something? The Candidate?
But hey, maybe the myth of Pandora's Box could have been an influence here... (And no, I'm not saying the Island IS a box. Let's not get into that whole 'the-magic-box-is-real' deal again...).