Sorry if this has already been mentioned - it strikes me as something that probably has. But hey:
What if the Island sunk because MIB defeated Jacob? Maybe his ultimate goal is to get rid of the Island/make it inadequate (for lack of a better word, but you get what I mean). I just thought about how people have likened Jacob to God and MIB to Satan. Jacob in Power = Island above water (like heaven). MIB in Power = Island underwater (like Hell). (Just to be clear I'm not saying they are God/Satan).
And maybe in timeline 2 our heroes will have to save the Island somehow and raise it up again?