Rory and Amy run to find the Doctor's body from twelve minutes ago, but it's gone. River assures them that he's not really dead -- "Rule one: The Doctor lies" -- and that the Dalek is dealt with. (Still shivery.) So then they run back to the Pandorica, where the nearly dead Doctor has locked himself once again into the Pandorica, turning the whole rooftop situation into another clever time-loopish moment where everybody else (including himself) was running around with Dalek and the fez and all that, so he could come down here and set things up for whatever's going to happen next.
That's when the room starts fading. First the objects, and the world outside; soon, everything. The Doctor's still too fucked up (looking fine, though) to really carry on a conversation, so he just sort of slumps in the Pandorica and mumbles about Big Bang 2.0, which is when they restart the universal engine using the old TARDIS and then Amy brainwaves everything back into existence (I think). "The TARDIS is still burning. It's exploding at every point in history. If you threw the Pandorica into the explosion, right into the heart of the fire, then... Let there be light. The light from the Pandorica would explode everywhere at once." Ah, the restoration field, right; we haven't gotten to the Amy part yet. So he's going to use the manipulator to pilot the Pandorica into the heart of the exploding TARDIS, which will then power the Pandorica sort of scribbling over all of space and time and fixing everything.
They stand in a bright red light, outside the Pandorica, as the world dies around them. Amy bitches at Rory for a second, and he just hugs her, because this is all quite sad. So but then what, as far as everybody in the room currently? They all wake up where they ought to be? None of this ever happens, and they don't remember it? Surely the Doctor can't possibly survive, Amy shrieks, and River sadly confirms it: "All the cracks in time will close, but he'll be on the wrong side. Trapped in the neverspace, the void between the worlds. All memory of him will be purged from the universe. He will never have been born." That sounds just terrible! I am sure that won't happen. River is very sad, bringing Amy into the Pandorica to say goodbye; she doesn't have much to say to him: "He doesn't really know me yet. Now he never will."
That is, to me, a lot more moving than anything that goes down with Rory, although there are a lot of times -- like right now -- that watching Amy be sad is nearly too much to take. She heads inside, crying and afraid to even look at him, and he smiles up at her. "Amy Pond. The Girl Who Waited. All night in your garden. Was it worth it?" Of course it was, she spits, afraid she'll start crying. "You asked me why I was taking you with me and I said... No reason? I was lying." He explains he's not being weird or maudlin: There are reasons, and there are reasons. "Amy, your house was too big. That big, empty house. And just you, and Aunt Sharon. Where were your mum and dad? Where was... Everybody who lived in that big house?" She can't remember. Her parents never were. Her loneliness always was.