Please read with an open mind. I believe I have found a grand, somewhat unifying theory for Lost. While it doesn't explain everything, I believe it goes a long way to relating to "the war" and other mysterious happenings.
In one of Walts flashbacks, he is shown studying a book of Australian native birds. After getting angry that his step-father Brian "wasn't looking" at him, a bird, an Australian Bronze Cuckoo, is shown flying into a glass door and dying on impact. Then much later on, on the island, Juliet inferred to Ben that Walt had killed a huge group of birds, and took Ben outside to see a pile of dead birds. So we can pretty much take it as a given that for some reason, Walt seems to attract birds in a magnetic-like fashion, only for them to die when they come into close proximity of Walt.
Now remember that Ben kept insisting to Juliet that Walt was special, and that Jacob wanted Walt to be with The Others. However we now know that Ben has never met Jacob, and it was infact MiB giving Ben these orders. So we can deduct that it was actually MiB who wanted Walt in close proximity to The Others. The question we have to ask ourselves, is why?. Well here is why: MiB wanted Walt near the Others, so that Walt might stay on the island, and bring about the demise of the Hurley Bird....
Whilst in the dark territory, in Exodus Part 2, Hurley saw a huge green bird, which we now know as the Hurley Bird. http://lostpedia.wikia.com/wiki/Hurley_bird. Hurley and some other Losties also saw this bird again, in Live Together, Die Alone, where the bird seemed to screech Hurley's name.
There is some huge, as yet, unknown spiritual presense attempting to communicate with some of the more "special" of the 815 survivors. The Hurley Bird is trying to reach out to Hurley. Much in the same way that the mysterious figure in the cabin who screamed "Help me" at Locke, was trying to reach out to Locke for help. If you go to the whispers transcript pages, you will also see that in the early whispers, there is a Woman-whisperer who often asks her other fellow whispers if they should talk to the survivors. She always gets reprimanded for wanting to reach out to them. But I believe she is part of this unseen spiritual force which is trying to reach out to our survivors.
When Jacob says "They're coming", I believe he is talking about these unseen spirits. As I've said, MiB wanted Walt to stay on the island. MiB knew Michael was attempting to leave the island, and many others would follow suit. However, MiB needs to plot the demise of the Hurley Bird, as this bird is just one of these so-called spirits that are part of the "light side".
There is more evidence to back up the theory of these spirits. The Hurley Bird, seen here: http://lostpedia.wikia.com/wiki/Hurley_bird, bears an uncanny resemblence to 'Altjira', the Australian aboriginal god of dreamtime. In Australian Aboriginal mythology, The Dreaming or Altjeringa (also called the Dreamtime) is a sacred 'once upon a time' in which ancestral Totemic Spirit Beings formed The Creation.
It was believed that, before humans, animals, and plants came into being, their 'souls' existed by themselves; they knew they would become physical, but not when. When that time came, all but one of the 'souls' became plants or animals, with the last one becoming human and acting as a custodian or guardian to the natural world around them.
The part I have placed in bold I find extremely significant. Read over it again if you wish... It could be that the whispers on the island relate to the souls of Dreamtime, and the whispers represent "souls" before they come into physical being. These souls are pure of being, and thus on the "light side", which Mib opposes. As the quote in bold states, one of these souls also becomes human and "acts as a custodian or guardian to the natural world around them".
This is reflected in Lost, however, it seems that there is not one such guardian in Lost, but two guardians. These two forces have split apart. Jacob is the guardian of these Lost Souls, and represents "light" however, MiB/Smokey, is the physical guardian of the island, and represents "dark". Over time, these two forces have grown further and further apart in ideology, and have come to oppose eachother. However, I do believe that the whole point of Lost, come to the end of the show, is not that either light or dark wins, it is simply that balance is restored to the island, and thus to the universe. How this happens in actual story telling terms, I am not sure, but I believe "the war" will be between light and dark, and will result in a grand union of light and dark, that restores balance to the island, and the two warring guardians of old (Jacob and MiB) will be replaced by the one true guardian, the guardian that brings balance. In other words, "the one who will save us all".