Neither Jacob nor MIB are completely evil or good and theories about their origins
Maybe the blonde boy is Jacob and he killed someone. Maybe they are brothers and Jacob killed their father and that’s why the boy had the hands full of blood and that’s why their mother got crazy.
Possibly Jacob feels regret for murdering and that why he decided to spend the rest of his life on the island. MIB lost someone he loved, in this case his father and feels anger and disappointment about all humanity for it. Jacob wants to repent for his acts and decided to show his brother that he can be good and that humanity is good too and he won’t let him go until he proves his point and his brother forgives him.
MIB is not evil, but he can’t stand his brother, that’s why he wanted to kill Jacob so badly and he is also desperate after being stuck for more than one thousand years in the island.
Jacob appears as a kid to MIB to disturb him. It is Jacob appearing as a ghost to make him give up on leaving the island until he shows that people can be good.
Jacob is not completely sane and is quite bipolar as can be noticed when he attacked Richard. He acted completely differently from his messianic behavior in other appearances. That’s why he likes to torment his brother with his appearances as a boy, reminding him of what he did. He also possibly made MIB lose his body and gave him the smoke appearance, but I don’t know how. Jacob created those rules and one of them is that MIB can’t reveal their true motives. That’s why MIB seems to be more sincere than Jacob, but he is unable to say why he does the things he does.
I’m not sure as this is exactly what happens, but I wouldn’t be surprised as something like that was true and neither Jacob nor MIB are completely good or evil. I get the feeling most of the time that MIB is a victim and he is so desperate to be free that he doesn’t mind killing or taking whatever action is needed to leave the island, his brother Jacob and his smoke form behind.