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In the final confrontation. Desmond was the only person who could go down into the light and unplug the cork. By unplugging the cork. The island lost all power. When the island lost all power ALL THE RULES COULD NOW BE BROKEN. Smokey/MIB lost all of his powers which made him mortal again but at the same time he could now kill the candidates directly. At the same time the island without its power was being destroyedprobably the whole world was being destroyed like Mother told her kids on what would happen if the light went out.
So MIB was now mortal and after a confrontation with Jack, he was finally killed. But the island needed to be re-plugged. Jack did this and sacrificed himself for the island. Hurley was left to be the new Jacob and Ben was his new Richard It appears that they had a successful long future not unseen but as Hurley told Ben in the ALT (which I am going to get into) you were a good number 2 Ben: you were a good number 1 As for the people on the plane it appears that they escaped the island and probably lived happy lives back in the main land. The ones probably back in the island lived happy lives, like Rose Bernard, Cindy and the kids. As for Desmond he probably was able to get back to his family as well thanks to Hurley and Ben. Jacks dying body was thrown out of the cave (like MIBs body In Across the sea). He laid there dying looking up when Vincent came over and as he looked up and saw that the Ajira plane had been able to leave. He closed his eye and died.
Eventually like everyone does, they all died, from old age or however. (including Richard who started to finally age). Hurley probably died long after everyone else once he found his own candidate. When they finally died their spirits joined the others who had died before during the course of the series, they were in this type of purgatory which in season 6 was the ALT reality. Once in this purgatory, once they woke up or realized that they were in reality dead. They were able to cross-over probably to a type of heaven depending on your spiritual views. They lived happily ever after, in the great beyond.
As for any other unsolved mystery? How about Walt? Aaron? Hurley bird, the outrigger chase scene. Some answers may yet be solved in the extras during the DVD release. And a lot of answers are already answered. Aaron was never special, Walts story was over in season 5. All of the weird visions people (like Walts random apparitions) were probably just MIBs turning into them.
People might not like this purgatory ending but we have to realize that everything that happened season 1 - 6 on the island was VERY REAL. Everything happened. The only thing that was purgatory was the ALT reality, and I strongly believe this was a joke of sorts from the writers. People from all the way back in season 1 kept theorizing that it was Purgatory all along, well the writers played an ironic story on us, we wanted a purgatory storyline, they created it..it was the flash sideways. Honestly this was the perfect ending cause we will be able to theorize for decades to come but more importantly our characters got closure and thats what LOST was truly about it was about the characters finally finding redemption and in the end, even if it was in the ALT/purgatory worldthey finally found it. ...Except for poor Micheal who is stuck for all eternity on the island as a whisper, for the sins he committed. But at least for the most part all the characters got a happy ending