The bomb detonates. The candidates are thrown back to where they came from. But where they came from is not the “real” timeline anymore.

In LA-X, the alternate timeline created by Jughead, we see how the candidates lives would have gone without Jacob’s touch and interference. Some things are the same, because destiny is a powerful force. Some are different, for better (James) or worse (Rose).

But in this alternate timeline, Jacob died and the island sank during the 70’s. Some of the Dharma Initiative escaped. Amongst them, Jacobs brother. Wearing the flesh of a dead man, trapped in a body which can no longer heal.

Just while the audience thinks the alternate timeline is the happier one, the better one, where the candidates are living better lives, we see Lockes father finally die. And Jacobs brother escapes from that fleshy prison that had been his tomb and everyone in that world dies at his hands.

The audience now knows what’s at stake, back on the Island. If Jacob’s brother escapes, the world will end.