hmm, my current theory, it's the island v the rest of the world. jacob & other man were the custodians. possible other man is the black smoke, but not sure.
throughout time, people have been coming to the island, but jacob's job is to protect the island. presumably, therefore, everyone he chose has a purpose there to continue the life of the island?
so jacob = good, other man = bad, trying to help people invade the island.
people who know what's in the shadow of the temple = jacob's followers (weren't they the people who warned miles not to go to the island after he was offered millions to go)
which makes all the others & dharma people unwitting accomplices to the other guy (don't think we saw jacob visit any of them, so not 'invited')
so, detonating the bomb may have negated the last 3 years, except that jacob's murder could add a little twist.
wondering if jacob allowed himself to be murdered, in a christ-like sacrifice (very biblical name), but also puzzling how all the egyptian stuff comes in. could the island represent the garden of eden, and the two men at the beginning be like cain & abel OR is it meant to be some 'lost' part of egypt (keep thinking about the statue), which needs to be proteected?