Things aren’t looking good for the Doctor and his friends. The Doctor is sealed in the pandorica. River’s trapped in an exploding TARDIS that is also destroying the universe except for Earth. Amy has been shot by an Auton version of her fiancée, Rory Williams. Rory-who believed he was the real Rory-is cradling her, and it seems there’s no hope.
And then, the Doctor appears. Holding a fez and a mop.
Turns out that this is the Doctor from some point in the future, who has escaped the pandorica somehow. How? Well, he hands Rory his sonic screwdriver before vanishing, which is then able to free the ‘present’ Doctor (as the Pandorica was designed so that people couldn’t escape, but it’s fairly easy for somebody to get in). The Doctor and Rory then put Amy in the pandorica, which will heal her injuries.
The Doctor uses River’s time-travel device (Similar to the one Captain Jack used) to jump to our present, which, due to the stars being destroyed, is somewhat different. The Doctor once again meets the younger Amy, and they reunite with her older version and Rory-who has been guarding the Pandorica-and Amy-for millenia (As an Auton, he’s ageless) at a museum.
They also free River, who has been stuck in a time loop in the exploding TARDIS, which has been acting as Earth’s sun since all the other stars are gone. The Doctor then uses the manipulator to jump into the past, to give Rory the screwdriver to free himself.
Unfortunately, a stone Dalek-reactivated by the Pandorica-causes some trouble for our heroes, zapping the Doctor before being destroyed by River. The Doctor then goes into the Pandorica, theorizing he can heal the universe by taking the remnants of the original Pandorica into the exploding TARDIS. This will also seal the cracks in time and restore what’s been lost.
The Doctor goes backward in his own timeline, repairing the cracks. He stops by at two points to tell Amy to remember him, before stepping into a crack himself, possibly erasing himself from existence.
Amy’s wedding day. Rory (now human again) and Amy attend but they both can’t shake the feeling they’ve forgotten something.
At the wedding, Amy’s memory of the Doctor begins to surface-and she summons him by doing so (as the cracks don’t totally erase people 100%).
“Something old, something new, something borrowed, something blue”.
The TARDIS then materializes at the wedding, complete with the Doctor and his ship fully restored-and in a hat and suit.
At the reception, the Doctor congratulates the happy couple, but he’s still bothered by certain unanswered questions. River stops by, and he’s still not sure as to her exact identity, and where she fits in his life. Perhaps more disturbing-the “Silence Will Fall” voice which started the whole mess in the first place, and which destroyed the TARDIS.
The newlyweds and the Doctor then board the TARDIS for future adventures, with the Doctor answering a phone call about a mummy on the Orient Express.
“Hello? Oh, hello! I’m sorry this is a very bad line. No no no. But that’s not possible. She was sealed into the Seventh Obelisk. I was at the Prayer Meeting. Well no, I get that it’s important. An Egyptian goddess loose on the Orient Express. Yes, your Majesty. We’re on our way”.