First clue: Jack mentions his father twice in the episode: once at a pharmacist when he tries to fill a prescription ostensibly written by his father, and a second time when, after the new chief of surgery asks Jack how much he’s had to drink, Jack tells him to get his father down here to see who’s more drunk.
We know Jack’s father to be dead; picking up his body from Australia was the whole reason he was on the plane that crashed. Both references could be explained away by of Jack’s decline into drinking and drugs.
Or . . . Jack’s father is alive when he shouldn’t be.
Second clue: Several episodes back in last season, in the episode titled “The Brig,” Naomi falls from a crashing helicopter with a parachute. When it’s explained to her that the island’s inhabitants are the survivors of the crashed Oceanic flight, she says that’s not possible because the crash site was found and submersible robots confirmed all the bodies were on the plane.
Again, you can explain that in various ways. Maybe it’s a cover up, maybe Naomi has a reason to lie, etc.
Or . . . our crew on the island appears to be alive when they shouldn’t be.
Two instances last season that reference people who shouldn’t being alive as alive.
Third clue: The last episode of last season was called “Through the Looking Glass,” a reference to the Lewis Carroll’s indentically titled sequel to Alice in Wonderland. In Looking Glass, Alice passes through a mirror into an alternate world where everything is backwards or at least off-kilter. At least so far, the “Through the Looking Glass” episode marks a turning point in the Lost narrative structure, specifically the replacement of flashbacks of the castaways life before the island with flashforwards of some of the castaways life after the island.
Fourth clue: At the end of the “Through the Looking Glass” episode, Jack meets with Kate. Both have been rescued, and Jack is apparently not dealing with it well. He tells Kate they weren’t supposed to leave and that he’s looking for a way back to the island.
Conclusion: the island is some sort of nexus between parallel worlds. In the castaway’s world, their plane got caught up in . . . well, whatever the event was that Desmond triggred, and that caused their plane to crash on the nexus/island. In Naomi’s world, Oceanic 815 crashed into a trench and all the bodies were identified. In the world that Jack, Kate, and Hurley escape to Jack’s father is still alive. And so forth and so on.
It doesn’t wrap up everything in a neat little bow. Like it doesn’t explain the wacky smoke clouds, the polar bears, Jacob, Locke’s healing abilities, the original inhabitants, etc etc etc. But it is an operating theory. I’m now interested in going back and watching some of the old episodes to see if I can pick up on other clues.
Ah, good old, narrative analysis. It’s like being an English major again. ;-)