One thing that has bugged me since mid-Season 5 has been where the Man in Black came from before appearing from the bushes in "Dead is Dead" right after Ben summoned the Monster. I think one possible explanation is that he assumed Smokey's form, made his way to Hydra Island and murdered the passengers. I believe the crew on Widmore's sub could not have killed these people since their bodies appear to have been well decomposed before Widmore's arrival.

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