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In the episode The Big Bang we see that the Doctor was in the Pandorica but was released by Rory and Amy was put in his place. He did all this by coming from the future with the help of a vortex manipulator.

Where did he get the vortex manipulator? He didn't have his TARDIS? He was stuck on Earth in 102 AD.

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Put simply, he picked it up off the ground after River left it there, presumably on his instruction.

There is a scene in "The Pandorica Opens", right before the Doctor gives his big speech to the aliens that are descending on Stonehenge, which shows River on a horse asking the Doctor (via communicator) if he has a plan. It then shows the Doctor on the ground next to the Pandorica, scanning it with his sonic screwdriver. Right next to his head, the vortex manipulator can be clearly seen.

This is followed up on in "The Big Bang", when the Doctor is shown picking the manipulator up after being let out by the Auton copy of Rory, which he then uses to jump ahead from 102 A.D. to the museum in the 1990s.

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The vortex manipulator was given to him later in both his personal timeline and the "universal" one, by River. Then he used it to go back and ensure that he was released, so that he would be able to collect the manipulator in the first place. It's a stable time loop.

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    I should note that an STL is not the same as a paradox, though they are sometimes treated as the same thing. A paradox is self-contradictory. This, while it would decay into a paradox if interrupted, is not - and, of course, it can't decay into a paradox, because there's no reason for things to happen differently on any given "iteration" of the loop.
    – Darael
    Jan 25, 2014 at 10:26

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