Sorry if this has been posted before but my new theory is that the others (the ones that took walt) are in another bunker on the island. On the video they said one of the things the project set out to do was a sort of mind control one (can't remember the exact name), and they had a girl between two conductors. I'd say thats the bunker they are in and they are still doing tests. We already know Walt has some sort of powers and thats why they were after him.
Oh and that Anna Lucia needs a kick in the teeth.