MIB is Cipher from New Universal by Locke4God

You probably have no idea what the F the title of this theory even refers too, but if you read comics you might.

New Universal is a recent series that features a lineage of people who have specific abilities and every so many years people with those abilities are recreated. One such set of abilities is attributed to an individual named Cipher. Cipher is the legacy name and the abilities she possesses are to be able to decode and work out complex equations and machinery on instinct. In other words, if it's physically possible to do, she can figure out how to do it.

A previous incarnation of Cipher developed electrical wiring that pre-dated ancient Rome. This newest version is struggling to build an automated body suit, but after gaining her powers, it becomes clear to her how to code the software in order for it to work.

Now take MIB.

He instinctively knows the rules of the board game he found on the beach. He is somehow aware of how the island's light can be manipulated to transport him off the island. He just knows, and can figure these things out, even without the base knowledge that an otherwise intelligent person would need to accomplish the same thing.

What does it mean?

It means he is special. He has a communion with the Island, stronger than anybody else's we've seen. He understands the island and can figure it out. Walt has some similar premonitions, but I'm not sure that he was ever quite as special as MIB is. Desmond certainly has a deep connection with the Island's power source. But MIB, no doubt has abilities that few others even come close to exhibiting, and that I think that means he has more of a connection than anybody.