DARK AND LIGHT

If you believe that the context of the show is a variation of an Egyptian myth, one of the most powerful stories was the journey of Ra, the Sun god, through the underworld each night. Ra's power was that of the sun (day light). But as the sun passed into darkness each night, it was told that it was because the sun god had to make a journey through the underworld, then after a successful voyage, return to rise the next day. In the underworld, Ra would be challenged by the god of darkness who would want to kill Ra in order to seize the entire world. During the journey, Ra would be helped by lesser gods and aides who would fend off attacks.

It was interesting to note, that Flocke waited until night fall before demanding to see Jacob.
And when we first saw Jacob in the base of the Tawaret foot, he appeared cowering in the corner of the room, afraid. This would be consistent with the theory of Ra, being a solar god being only powerful during the daylight. At night, he would be open to attack. One of the rules could be that Jacob is light and MIB is dark; and their full powers manifest themselves during those passages of time.

As also speculated, it appears that Jacob and MIB are rivals, but may not be able to directly kill each other. MIB needed to find a loophole. That is why Flocke (MIB) got Ben, a loyal follower, to turn and kill Jacob.