So far we have witnessed time travel and flashes that were caused by the electromagnetic properties of the island and put in motion through the frozen donkey wheel. Though we were told that the principals had hoped to harness and control the time travel capability, so far we have not seen evidence, only small experiments. At some point in the future, some person or people will be able to purposefully travel back in time and influence the events as they know them. I believe Jacob is that entity. He was there for every turning point in the Losties' lives that led to their being on flight 815. Widmore and Ben have been told what is to come. However, Ben seemed genuinely distressed when Widmore murdered Ben's daughter, thereby changing whatever rules were set up by their masters. On the freighter, Keamey went to the secondary protocol because he knew that Ben was heading to the Orchid and could be found there. When Locke left the island, Widmore told him of the war that is to come and that he must convince everyone to go back or the "wrong side will win." How this all plays out is anyone's guess, but I sure am anxious for the new season to begin.