MiB's Real Identity and Möbius Strip Theory by Albert Awol

The end of one timeline is the beginning of the other, ad infinitum. There won't be any moment in the show that you could actually call a beginning or an end. The "alt timeline" that is created by the island being underwater when 815 zooms past has peppered throughout it butterfly effects prior to that passing. In fact, due to the jughead explosion in the 70's, things happened different in the 50's. This new timeline will lead not to the end of the game, but rather the beginning of it. The little boy is Jacob of course, just not in sequential order. Considering all the foresight Jacob has, it should be obvious that (considering the lostverse permits timetravel) he is originally from the future. This new ALT world without jacob will give way to the ORIGINAL timeline when young Jacob (who now can't be killed until Ben does it in his future making him invulnerable like other characters had briefly been) tricks Locke! into being drawn into the distant past with him.

Picture the lostverse timeline as being one big long loop with a twist in it. You can move "forward" in time infinitely, but not to the past. The arrow of time never changes, but time itself loops back around to the beginning. You can "go to the past" by flashing far enough into the future to make it all the way around the Mobius Strip again. You're not really in the past... just far enough in the future to appear to be. This is what happens when you time travel on a Mobius Timeline.

So who is MiB really? How did this guy impersonate Locke? And why is it Locke's body that he's now Locked into? Well there are TWO Locke's now. The one that dies each iteration and the one that gets pulled into the past with Jacob. Over and over each pass around the mobius strip. But the reason John Locke is "special" is that he IS MiB. Originally. The MiB we know and love... the smoke monster... body snatcher... game player... before he was all that was none other than... John Locke. We have the young John Locke who dies each iteration (possibly preventing Jacob from taking that Locke into the past) and the Original, super duper first John Locke who has traveled the Mobius Timestrip so long that it wouldn't even be fair to call him "John Locke" anymore. From his perspective, he could be tens or even hundreds of thousands of years old.

It might have even been fun the first couple of trips around the strip... setting himself up as an Egyptian God and basking in his now innate invulnerability. (Can't die if it's destiny to be looped around again by Jacob) But like anything, it gets boring and he's now desperate to get out.