Locke's trek with Ben and Hurley results in them finding Jacob's cabin again. In the cabin, John sees a familiar face. Meanwhile, on the freighter the crew is divided as of what to do.
As Keamy opens the safe on the ship, he gets a printed protocol which has a Dharma logo as a cover. This would suggest that the Dharma Initiative is still active and that Charles Widmore is either in charge of it, or at least in some way connected to it. This would also explain why Widmore said to Ben that Ben took 'his island'.