Interesting theory came up today BS'ing about the finale.
Could the ship belong to "Dharma", who are coming to get their island back? Not much else would scare Ben like that, IMO.
Perhaps next year opens with Dharma Helo Gunships strafing "The Others" to the tune of "Ride of the Valkyries" played on a Sitar. Oh, and "Namaste, MF'rs" displayed on the Helicopters rocket pods.
As for Jacks father? We were thinking the island is a nexus between two parallel universes. In one, Oceanic Flight 815 crashed in the ocean, in the other, on the Island. That might also account for Oceanic still being in business in the flash-forward, while "The Lost Experience" (considered canon source) stated Oceanic went out of business. Perhaps the survivors "passed through" during the "event" when the Hatch imploded.