so, I feel this thread should be revived for mid-series theories, now that they should be plentiful and entertaining. I have one theory, mainly to do with the Silence, but is kind of a guess at the arc story. So, the Doctor rebooted the universe. The whole universe. Well, even though its sealed off, the Time War and the society of Time Lord are part of the universe, and so all of that was rebooted as well. In the End of Time, there was a very important line about the Time War; "You weren’t there in the final days of the war. You never saw what was born. But if the Time Lock’s broken then everything’s coming through, not just the Daleks, but the Star of Degradations, the Horde of Travesties, the Nightmare child, the Could-Have-Been-King with his Army of Meanwhiles and Never Weres – the war turning to Hell!" The last bit of that quote sound very much like the Silence-esque deal. SO, I feel it makes sense that the Silence are leak through from the time war, probably drawn out by the same person/people who cause the TARDIS to crash and cause the reboot. Also, a bit from classic who: The creators of TARDISes were Rassilion and Omega. At some point (I'm not very fluent in this bit, as I haven't watched all of classic who) There was a super nova (or bloack hole collapse, or something like it) and Omega was caught on the wrong side, and was thrown into into pocket universe. SO, the Universe got rebooted, whoch mean the series of events that led up to Omega's universe happened again, but the original pocket universe would not have been touched, which would result in all variety of Timey-wimey fun stuff for Moffat to play with. Also note that the symbol for the New Church, as seen in the Time of Angels/FLesh and Stone and in A Good Man Goes to War is an Omega. Thats my theory. Y'all?