So I was chatting with Becca and one of her coworkers today at lunch (on wifi from the local BBQ dig  ). We came up with a great theory:

When Ben went into the little room, he actually went into a teleportation device (the black box that brought Lock's dad, perhaps?). That's how he ended up in the Sahara desert with no tracks. This is supported in that the two guys who came to him apparently said something about there being no tracks in their foreign language. The change of clothes? Well, there were clothes hanging in that room Ben went into.

So anyway. The teleporter put him into the past or future or something, and those guys he killed were actually the very same guys who were on the island to kill him. And this is what unleashed the black smoke - the black smoke is actually a kind of 'course correcting' thing that happens on the island. Since these men were killed in another time off the island, the black smoke 'corrected' it by killing them ON the island. It would make sense... the black smoke could be like a rift in the space-time continuum that is 'forcing' a course correction to keep the universe from tearing apart (thanks Doc. Brown!). I'd explain the little flashes of images as things that happened in someone's past/future/present that are manifesting as the black smoke is 'correcting' something.

Also, why can't Ben kill Whitmore? Perhaps Whitmore is Ben's constant!

Anyway. Just some theorizing...

I'm a much bigger fan of the whole possibility of there being timewarps/temporal wierdness that is explained scientifically.

Jack DID try to kill himself. He was going to jump off the bridge, but he got 'side tracked'. Technically, you could say the island won't let him die.

That could be interpreted as Fate.