My biggest criticism of the episode comes from the first act. at the end of episode one, they traveled from the oval office to florida in the TARDIS. After Amy shot the astronaut suit why exactly did they have to go on the run for three months? Why not just retreat to the TARDIS? and how the hell did the TARDIS end up inside the Doctors cell at area 51 anyway?
I think this is a major problem with the two-parter.
As
Lonemagpie noted several pages back, the plot doesn't really kick in until the start of this episode, making "Impossible Astronaut" largely superfluous. (I think it's mainly the backstory that simply wouldn't fit "Day of the Moon" myself.) The three month jump is a bit convenient for Moffat -- not only does it jump-start the story to an
in media res position (which "Impossible Astronaut" did not do), but it also allows Moffat to gloss over his plot problems. If something doesn't make sense, you can simply say, "Well, that happened in the three months we didn't see."
Team TARDIS going on the run? The Doctor imprisoned? Canton's loyalties questioned? All "explained" by the three month gap. I've rationalized these problems to my own satisfaction -- clearly, the Doctor formulated a plan at the warehouse, sent Amy, Rory, and River on their way, put the cloaked TARDIS in Area 51, and had Canton "capture" him so he could imprisoned and he could plot away to his hearts' content. The problem with this, however, is that it assumes that the Doctor understands more about the Silents then than he does at any other point later. (It doesn't explain why the Doctor goes instantly to genocide as a plan, however.)
It's a very New Adventures-esque Doctor. He's playing a long game, and he's doing it in such a way that even his closest associates don't have a clue what he's really up to.
Did the Silence really do anything bad besides look creepy? They did kill that one woman in the bathroom, but besides that, what did they do wrong?
That's still bothering me. We don't even know what the Silents wanted, which is what's so appalling about the Doctor's plan to exterminate them. Was there anything the Silents did that justified the Doctor's brainwashing of humanity to murder the Silents on sight?
My gut feeling is that the Doctor erred badly in 1969. He may have jammed a stick in a hornet's nest by making a disproportionate attack on the Silents, and that could be why the Doctor has to die in 2011.