Right on time, the Doctor appeared, looking lovely in a fez and holding a mop. He babbled at Rory for a bit, you know, about how dead Amy was not the end of the world -- although it was the end of the universe -- and then blinked out again for a second, scaring Rory to pieces. (That black sky, I must say: Very disturbing.) The Doctor asked Rory to get him out of the Pandorica, which if you can do that crap why even bother to have a time travel story, but whatever: He handed Rory the sonic screwdriver and asked him to leave it in Amy's pocket, for later.
The Doctor was surprised, to say the least, when Rory freed him from the Pandorica. (I guess moments after he was put in there, considering the entire universe ended at the end of the last episode.) They got variously weird with each other about the sonic, since now they both have one -- sparks when they touched them, tip to tip -- and the Doctor remarked that it was nice to know he had a future-self to give Rory the sonic anyhow. He explained further: "History has collapsed. Whole races have been deleted from existence. These are just like after-images. Echoes, fossils in time. The footprints of the never-were. Total event collapse. The universe literally never happened." So then why were they all hanging around at Stonehenge, dressed like this? "Eye of the storm, that's all. We're just the last light to go out..."
Rory at this point sadly explained to the Doctor about killing Amy with a shot right to the gut by his robot gun-hands, and the Doctor was like, "Oh, Rory!" He explained what Rory was, what we'd already figured out: He was a "Nestene duplicate, a lump of plastic with delusions of humanity." Rory protested that he was no longer that sort of thing -- "I'm Rory now," he shouted -- but whatever. "That's software talking." The Doctor pissed Rory off a little bit at this point, talking about how he didn't really have the time to fix it because of the universe ending, and then things got pretty annoying with Rory punching him in the face and screaming about love and I guess turning into a Real Boy just like Churchill's robo-doctor from before. Or maybe he said "to blave," which is as everybody knows an archaic verb-form for "to bluff."