Part two of last week's episode, and again the plot barely exists, so I'll just mention a few things as they occur to me rather than going through the plot point by point.
The Doctor, Amy and Rory arrive on a pirate ship, apparently because of a distress signal they received. The distress signal will be relevant later, but given how often stupid shit like that happens in this show for no reason there's no way to guess that.
This episode opens with a complete waste of time where they pretend they're on the run and the Doctor has been captured and imprisoned in Area 51. It's not at all clear why they felt the need for this ruse. There doesn't seem to be any reason for it at all, other than to waste some time.