Daniel Faraday returns to the island with the scientists on the submarine

At the pier where the submarine is docked, Miles is helping unload luggage from the sub. Behind him further up the pier, Stuart Radzinsky and Pierre Chang seem to be checking in the Ann Arbor scientists. Someone coming out of the sub puts a suitcase on the outside the port and asks for a hand with it. Miles comes over to help, picking up the suitcase then stopping when he see Daniel Faraday emerge from the submarine. Miles says in a shocked tone "Dan." Daniel says "Hey Miles. Long time no see." And that's it.

So how long was Daniel off of the island and how did he manage to come back with the Ann Arbor scientists? Hopefully we'll get to find that out in the upcoming episode titled "The Variable."