Ok guys this is really really long, but it took a lot of thought and looking up facts on Lostpedia.
So far, everything that has happened on Lost has been a constant battle between Jacob and his nemesis. I believe Jacob’s nemesis is the actual Island itself, which can manifest itself in many forms. So far I believe we have seen it manifest itself in the form of the bearded man played by Titus Welliver we saw at the beginning of the Incident Part 1, John Locke, Walt, Christian Shephard, the Monster, Alex, Yemi. It has appeared, with the exception possibly because he is special, the Jacob’s nemesis, that Jacob’s nemesis can only inhabit dead bodies to do it’s bidding. Jacob has been referred to as being in charge of the Island, so therefore he would have a superior role to his nemesis if his nemesis was a manifetation of the Island itself. It has appeared that the Nemesis is adverse to new people coming to the Island, (or if he really is an manifestation of the Island itself, adverse to people coming to him) as he didn’t approve of the Black Rock coming to the Island, and he told Richard in 2007 that they needed to “take care of” the rest of the Ajira survivors. For years and years Jacob has imprisoned the heart and mind of the Island in a cabin, the cabin that Ben wrongly thought Jacob resided in. At some point, either accidentally, or on purpose, the ring of ash surrounding the cabin that probably kept the Nemesis imprisoned was broken. It is quite possible that even though he was imprisoned, the Nemesis was able to communicate with people and beings on and off the Island. Charles Widmore and Matthew Abaddon played a significant part in bringing John Locke to the Island, and could have been working on behalf of Jacob’s nemesis. Widmore said, most illuminatingly, in “The Life and Death of Jeremy Bentham,” “…there’s a war coming, John. And if you're not back on the Island when that happens, the wrong side is going to win.” This war, in my opinion, is the war between Jacob and his nemesis. Widmore played a huge role in bringing Locke to the Island the first time around, and actively helped him return to the Island with the Oceanic Six in 2008. I believe the force guiding Locke through his journey on the Island was the Monster. By having Locke end up finding the Hatch, the Monster set Locke on the path that would eventually destroy the Swan, destroying the electromagnetic anomaly, making it much easier for the Island to be found. Widmore, whether or not he was working for the Nemesis or himself, found the Island and sent a freighter to reclaim it for himself. With these events coming to a head, under the guise of speaking on behalf of Jacob, Jacob’s nemesis as Christian Shephard told Locke to move the Island, knowing full well that Ben would try to gain the glory and turn the wheel himself, sending him off the Island, and sending Locke on the time skips instead. These time skips, in short, would establish Locke as the new leader of the Others. In 1954, he told Richard that he was the future leader of the Others, and he told Richard to visit him in 2 years to witness his birth, which started the (mostly untrue) belief that Locke was special, when in reality the whole time Locke’s specialness was engineered by Jacob’s nemesis. And in a very ancient time period (which I strongly believe coincides with the period we saw at the beginning of “The Incident Part 1”, for my theory on this see my other blogs concerning this) Locke went down to the Wheel Chamber and was met by Jacob’s nemesis in the form of Christian Shephard. Jacob’s nemesis, at this point in history, probably wasn’t imprisoned yet, and had some sort of super special knowledge of what would happen in the future if he met Locke in the wheel chamber. He told Locke to leave the Island, and bring everyone back, and that he would need to die in the process, as a sacrifice to the Island. Locke was only able to convince Jack to return before he was killed by Ben, but convincing Jack had a very effective domino effect on bringing the rest back. With Locke back on the island, dead, the escaped Nemesis was able to take his dead body’s form and assume the mantle of leader of the Others that Locke had left behind. As the imposter Locke, he was able to tell Richard to tell the time traveling real Locke to bring back the Oceanic Six, and that he would need to die, making sure that the start of the string of Locke thinking he needed to die was in place. (making the image of Jacob weaving his tapestry at the beginning of the season 5 finale all the more symbolic) The loophole, whatever it may be, had something to do with the fact that only the leader of the Others can get an audience with Jacob, or that Jacob’s nemesis couldn’t kill Jacob unless he was in the form of the leader of the Others. So by having Benjamin Linus kill Jacob, Jacob’s nemesis completed a “long con” that made Sawyer look like an amateur. I feel like in my analysis of all this, I have made Jacob’s nemesis aims and goals much clearer than Jacob’s. Jacob knew and wanted the Oceanic Six and Ajira 316 to get back to the Island. Why? Could it be that Jacob wanted Jack and Co. to wipe out the electromagnetic pocket of energy underneath the Swan so that Locke would never come to the Island, setting forward the chain of events that would lead to his stabbing by Benjamin Linus? His statement, “They’re coming” is most illuminating in this light. Jacob realizes that he may have failed at changing the future, and that he will die, and the consequences of his failure will mean that the Incident always happened as we saw it happen, and that Jack, Sayid, Kate, Hurley, Sawyer, Jin, Miles, and Juliet are coming back to the present time. For whatever reason, this may not be a good thing for Jacob’s nemesis. So my ultimate conclusion is that Jacob may have lost the battle, but he hasn’t lost the war. The future wasn’t changed, Locke always came to the Island, and always died, and always was taken over by Jacob’s nemesis, and Jacob was always killed by Benjamin Linus. But “they’re coming,” and this spells bad news for Jacob’s nemesis, and what season 6 will be about.