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.