Ben Linus is the ultimate long con man. He has been working with MiB this whole time to set things in motion to allow MiB to win. He told us a war was coming (we thought it was between him and Widmore but he was talking about Jacob and MiB the whole time).
Ben had encounters with smokey but was never injured or killed by it. Ben was the one who got everyone back to the island. Ben killed Locke and made sure his body was brought back to be a vessel for MiB.
Ben was brought back to life in the Temple and he is poisoned just like the Sayid and Claire. Also, it was Ben that used the MiB power to bring Locke's father on to the island. Now the question is, what does Ben get out of all of this?