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Originally Posted by Pierre
So all of the universes most evil races all team up to imprison the Doctor in a big box with lots of locks and things.
Then they all just leave......................
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No, they didn't leave. They were abolished from existence, because they attacked the wrong person (the Doctor), mistakenly believing that it was he that was going to blow up the TARDIS.
They thought that by imprisoning him forever, they could stop him from doing that. But they were wrong. The TARDIS was being attacked by an external force, the nature of which has not yet been revealed, but which has been set up as the arc for the next series. With the Doctor out of the picture, the TARDIS explosion took place and the universe began to collapse. When he was released from the Pandorica, the Doctor explained to Auton-Rory that the statues left in the ante-chamber were time fossils, echoes of things that never were ... or words to that effect.