Long and crazy post from TVTome :

I don't think we're dealing with a cloud of 'smoke' at all. Think about it. Danielle said it was the island's defense system. Locke treated with it, so it demonstrates some sort of sentience. I doubt it's supernatural in nature, although it has that appearance. So what is it? As I watched this thing uprooting trees, roaring, changing into various shapes and what not as need dictated, it hit me what it may well be: a cloud of nanites. Tiny robots, moving in a swarm, like bees or migratory birds, harmless alone, but all too deadly acting in unison. Literally, they would be like a living cloud. This would explain Locke's 'miracle'. They could have entered his body as he lay unconscious and repaired the damage to his nerve tissue, or, perhaps, left some of their number behind to bridge the gap, which would explain his later loss of nerve connectivity, and the visions. They could invade the host's brain, either disrupting its function, causing madness, or perhaps, in time, taking control entirely. Michael Chrichton wrote this cool book called "Prey", that deals with that very topic, namely, swarms of nanites originally developed for surgical applications, which evolved, developed sentience, and seized control of host organisms. They could be part of a larger machine intelligence housed beneath the surface of the island iteself, for which the hatch is but one egress. If this is the case, it explains why Locke refers to the island with a proper name, calling it "The Island" (the hatch, by the way, is awfully reminiscent of Morlock holes from "The Time Machine, isn't it?). Perhaps the 'pirates' that took Walt were part of this intelligence. Perhaps they were the Others, or part of their number. If indeed, they were from the party of scientists that crashed on the island with Danielle, that too would explain why they began to act "different", and how come Ethan, who would therefore be of that number also (could be Alex, as some have speculated), showed greatly enhanced strength, agility, and a sort of preiscience that union with a gestalt, machine intelligence created by or facilitated by networked nanites existing in symbiosis with their host would provide. So you see, it's all about the nanites, and a machine intelligence that killed its makers, and lured these people to this island, for purposes unknown...