If you haven't watched the new episode of LOST, stop reading because I'm going to toss out some ideas and questions.
I had guessed that the hatch led to a laboratory which controls the island experiments last season. Now I think that the experiments include disease which Desmond is taking medicine to ward off (or treat?). He looks a bit insane to me. He wasn't surprised to see Jack. The island has been sending out signals since WWII, so did Desmond take over for a previous group? Desmond is almost a doctor and it looks like he has the same special skills that Walt has so, did he bring the plane down because he needed Walt? Did he also bring down the drug plane? The pirates that took Walt were in a boat driven by a blonde woman and I totally missed that last season. Is Gabriel's child dead or one of the pirates? Do the pirates work for Desmond? The ship on the island predates Desmond's equipment doesn’t it? The image of Walt was only in Sharon's mind because Walt was communicating directly with her. He hushed her and then he said something. What was he trying to tell her other than to be quiet? There is something very odd about the dog that I can't put my finger on yet.
Also – Why is Desmond nocturnal?