John Locke will come back ... kinda by Thomas

So here's my theorie.

Let's start from the beginning.
Becomming submerged in the "light" is what turned MiB into the smoke monster, it is not what turned him evil. He was turned into the smoke monster because being submerged in that much light/power/life is too much for a human to handle so he became something else, something more powerfull. It also however trapped him on the island, he can not get away from the source of light. What turned him evil was his obsession to want to leave the island which he now can never do, unless he can destroy the island, which in turn he can not do untill the protector/candidates are dead.

It is the whole destiny vs. free will theme, it is his destiny to be on the island, this he can not controle. What he can controle is if he will let his destiny will make him do evil things, or good things. He could clearly never come to terms with his destiny(Jack's original state) and let it turn him to evil.

Now what I think happened and here is where the two timelines come into play. When Jack acted on trying to change his destiny by blowing up the H bomb, the second timeline was created (because of a confliction of the rules, Juliet can not kill the candidates, but it did destroy the island, so the candidates could not die but there was no island for them to be one, to correct this impossibility the second timeline was created).
Jack could at this time not accept the past and his destiny but he will correct this eventually in the original timeline. He will be confronted with trying to change the past again and letting the second timeline exist in which all those people did not die because of him, or accept it and make the right decision now.

MiB will be defeated using Desmond, because of his ability to resist the electromagnetic power out of which MiB now exists. After this has happened only John Locke's personality and memories will remain, and John Locke will be the new smoke monster. But as I said before, being the smoke monster does not make you evil, in fact, John Locke will be more than willing to stay on the island forever.

Lastly, Kate will be the new Jacob, Jack will die destroying the other timeline, Sawyer will die getting redemption and completeling his character evolution(only caring about himself to dying for others).Hurley is not a lead but will get a new role on the island.
Also this was hinted at heavily with the Valenzetti equation, all the numbers but hers lead to the end of mankind. Plus Jacob was able to deceive MiB into believing it would not be her, thats why she was scratched out in MiB's cave but not in Jacob's lighthouse.