Over on the forum, Exterminate, who is one of our members, has pointed out something interesting he spotted in the background of a photograph which may indicate that the Doctor is indeed being held inside Area 51 at some point during the opening two parter.
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The MIB to the left of the picture means we can definately link this photo to the opening two part story that was filmed in the US. In the middle, albeit faintly, we can see a chained up bearded Doctor and then on the back wall we can see 'A51' written quite boldly. It doesnt take an enormous leap of logic to assume that the Doctor is being held inside the famous containment unit, but as Exterminate speculated on the forum, could this also have something to do with the 'little green man' in a suit that we see at the end of the Series 6 trailer?