Jacob literally took the MIB's body giving new meaning to the loophole by Alan sAWCHUK

I think that one possibility is that the entity Jacob literally took the MIB's body when the MIB came to the island. There may be very specific rules that the MIB needs to follow in order to get his body back or in order to obtain a new body. He may need to win the "game" with Jacob before he can have his original body back trapping him on the island. He can't directly kill Jacob because killing that body would prevent him from possibly getting it back for himself. The loophole may be that the MIB can obtain a new body if he copies the body of a person who dies off island and is brought back to the island. Once that happens, he no longer needs his previous body now possessed by Jacob and can then devote his efforts and powers to killing Jacob's human form, which is able to keep the MIB on the island while alive and in a human body. Of course there may be rules as to how he can kill Jacob's human form. He may stil! l need another intermediary such as Ben to help him according to the rules of the game.

In this theory the need to find a loophole really means that the MIB can't kill Jacob since he would be destoying his own body unless he finds an unusual way to obtain another body, which needs to follow the rules of the game. In this instance neither Jacob or the MIB are good or bad, although there is a wager involved about the morality, destiny or fate of other people who are brought to the island.