Underwater Volcano
You know I’m completely unsure WHAT the smoke monster is…. I remember John saying something about there being a volcano on the island. Well, what if…. The island is underwater at some point and the volcano erupts. The hot molten lava explodes when it hits the cold sea water, producing thick, black clouds of steam and ash. Could this be the result of the smoke monster in some way? I’m not sure entirely like I said how this could happen, but it maybe. Anyway, let me know what you think!

Nah… Too elaborate. Let’s just go for the simplest possible explanation instead, which means… er… let’s see now…
Alright, if it’s not an alien nano cloud, it’s gotta be magic volcano ash. Those are exchangable ingredients in most recipes anyway.