First, to identify Jacob and the MiB as good and evil is shallow at best. Based on the logic and mythos inherent to the show it makes more sense to view Jacob and the MiB as conscious manifestations of the electromagnetic energy that is innate to the Island. The entire show is saturated with principles of dueling opposites, i.e. yin/yang, black/white, and an alternate universe. If we remember back to one of the earlier Dharma videos, the chief scientist mentioned the “dark exotic energy” that is in the core of the Island. Thus, it would follow that the MiB’s wanting to go “home” actually represents the desired “release” of the exotic energy. Jacob on the other hand, represents the magnetic opposite, that which attracts! Hence, Jacob attracting and influencing people to come to the Island; for further emphasis, if one reflects back on the initial episode that showed Jacob, you should noti! ce his “spinning of yarn.” This is a folk-metaphor to exhibit the strands of life, or that of elaborate deception, that are predetermined by fate. To supplement this idea just remember the names in the cave.
Since I am romanticizing the wonder of dualities, let me go one step further by putting forth the claim that those who exist in the alternate-universe are the exact opposite of those who exist in the original story line. They are the opposite, yet they are the same; this leads me to my boldest of predictions: Jacob and Locke are the same. They can’t directly kill each other, and once the nuke went off they cease to exist in the alternate-universe. WANT SOMETHING EVEN MORE MIND-BOGGLING: remember when they were both sitting on the beach and Jacob caught and ate the fish. The MiB walks up, sits down, and is asked by Jacob if he was hungry. The MiB says, “no, I just ate.” He just ate b/c Jacob just ate! In sum, in order to know what the Island, Jacob, and the MiB/Locke are one only needs to remember the book Jacob was reading, “That which arises must converge.” From that, I think I can deduce that they are all the same.
As a final thought, the thesis of this show seems to be, “It only ends once, everything else is just progress.” This seems to be right. One universe DID end via the nuke and created the two universes we are experiencing in this final season. However, these 2 “arisen” universes will converge. How so? The emotion and memories that are able to be transferred from one verse to another via any particular character’s “Constant”. This transference not only addresses the infinite dualities inherent to the show, but it also promotes a progress that is unending. After all, life really does end once.