I think the ship that is coming to the island is sent by the DHARMA company. I think this because when Locke was playing the chess game at the DHARMA station that they stumbled upon, he beat the game and it said to push the button if the hostiles took over, this was to alert the DHARMA company so they can send reinforcement, that is why Mikhail stopped john from pushing the button. I think the DHARMA company thought they were still running the operation on the island, but they were being fooled by Ben and the others. That is why they still got food and supplies drops. At the very end of the season I think Richard Alpert said the other people were worried about there food supplies. That is because DHARMA didn't drop any more food. I think when they get to the Island they are going to be hostile a kill all of the people so they can reclaim there island and start to fix every thing up and start their experiments again. The others and the people for flight 815 will join forces. I think that they will also use some of the islands unique features and the other DHARMA stations to stop DHARMA from taking over again. That is were we will learn all the secrets of the island. I also think Widmore Industries has some part of DHARMA, maybe they our a major investor in the DHARMA company.