Oh, so complicated. So basically, last week the entire universe ended and Amy was killed and the Doctor was put in prison and the TARDIS blew up with River inside it. Those are some long odds. But with a lot of narrative and time-travel complications, there's a pretty basic and very fucking charming story to be found here. Let's see if I can do it.
The jail thing is easy: Future free Doctor just blinks in to see Rory using River's vortex manipulator and gives him the sonic so that he can free the Doctor. (That's iffy, but whatever -- the universe ended so probably you can do shit like that this time.) At this point, they put Amy into stasis in the Pandorica so that her future kid self, Amelia (!) can give it a proper DNA model to revive her, which the Doctor arranges with all kinds of bopping around the continuum. Meanwhile, Robo Rory takes the long path and guards the Pandorica for the 2000 intervening years.
Now we've all met up again, but it's a strange world little Amelia lives in: As a pocket universe that's basically just like the leftover echo of the previous universe, it's missing things like stars. What you think is the sun is actually the Event that caused the Cracks: The TARDIS eternally burning up in the sky, with River inside playing out her death over and over and over again thanks to the TARDIS trying to save her life. The Doctor pops in and saves her, neglecting to explain that the Pandorica has also woken up a stubborn old Dalek that is about to kill him.
So it kills him, and River takes it out in a very scary way, and then Amelia disappears into the Crack, and there's a fair amount of running about before they realize that the Doctor wasn't actually dead: He was putting his nearly self into the Pandorica, aiming to vortex-manipulate it into the heart of the sun/TARDIS/Explosion itself. This will result in a fusion of the always-everywhere awesomeness of the TARDIS with the reconstructive powers of the Pandorica: A Big Bang 2.0 that will put everything right, including retrieving Amy's parents and things from the Cracks and generally making her a normal person retroactively.
Downside: The Doctor and the TARDIS will end up on the other side of those Cracks, meaning nobody ever met him and he was never born and River has no hot husband. Surprisingly, that's exactly what happens. (Although there's a typically cheeky moment where you can tell the Doctor's got another angle to play.)
The Doctor's life begins to unspool, giving him a limited amount of time to fuck around and taking him back through the entire season, particularly the two most important moments we already thought were weird: That time he cried and kissed Amy on the Byzantium, and the time Amelia waited all night and maybe got a visit from the Doctor that we don't know about. In the former, he begs her to remember. In the latter, he tells the sleeping Amelia a real tearjerker of a longshot, all about their time together and how the Raggedy Doctor was real, etc. Then he jumps into the Crack in her bedroom, healing everything and winking out of existence.
Wedding day: Between the coded dream-messages and River dropping off her TARDIS-shaped journal, Amy does more of that spooky crying-without-crying and finally remembers the Doctor, calling him back across the void with her Crack-given memory powers. He shows up in a tux, which is radical, and after the dancing is done he has a run-in with River Song, in which shit gets real.
The happy couple surprises him when he's trying not very hard to sneak off, and he points out that A) we still don't know what Silence is or B) why the TARDIS needed to blow up in the first place, and they decide to join him on his next adventure, which sounds typically baroque.
All in all, a lovely damned ending and a lovely damned two-parter that manages to take all the weirder things about this season and wrap them up in a strangely not-creepy bow. It's been a wild ride and I can't say it wasn't touch and go, but these last four episodes have really taken us in a newer, smarter direction. I can't even really remember at this point what I found so annoying about all this -- maybe it went with the Cracks. See you for Christmas?
"Every sun will supernova at every moment in history," the Doctor screamed, as they locked him in his perfect cell. 1894 years later, Amelia Pond sat in her lonely house, with its spooky overgrown garden, and asked Santa to help her with the Crack in her wall. Her parents were gone but she didn't know it. The ducks in the pond were never there. The TARDIS came, and gave her something better than Santa, or a cop, or anybody you could ask for.
She painted stars in the sky, like Vincent once did, and it scared the grownups, because there's no such thing as stars anymore. There never were. The universe was dark, all the time, it always had been, and nobody but Amelia remembered different. They took her outside, to show her the black sky, and she kept her mouth shut. She didn't bite them, not that time.
"I just don't want her growing up and joining one of those Star Cults. I don't trust that Richard Dawkins," one of them said downstairs, and then a mysterious and jaunty figure tossed a museum flyer through the mailslot: An exhibition of the Pandorica, the strange thing they'd discovered under Stonehenge, with a red pen's flourish pointing at the façade: Come along, Pond.
So she did. She dragged Aunt Sharon through the whole National Museum, past all kinds of science and history, soda in her hand, yelling Scottishly until she found some old stone Daleks, and then again into the Pandorica room. Aunt Sharon left far behind, as she smiled up at it. A jaunty trickster snatched her soda right out of her hand, and before she could see him she found a note on the Pandorica, at a perfect Amelia-height: Stick around, Pond.
So she did. I guess eventually Aunt Sharon got bored looking for her, and the people all went home, even the security guards, and she was finally alone. Alone in a museum is right up there with alone in a shopping mall, for things I had to personally realize I was never going to get to do, unless zombies happened. She made her way past all kinds of spooky nighttime things, and to the Pandorica. And when she touched it, it opened wide. The light shone down on her like first contact, and fell upon the stone Daleks, and sitting chained inside was a beautiful girl.
"Okay, kid," Amy said to Amelia. "This is where it gets complicated."
1894 years previous, Rory sat under a black and starless sky, with Amy's body in his lap, telling her the story: "So, the universe ended. You missed that. In 102 AD. I suppose this means you and I never get born at all. Twice, in my case." He asked her to laugh, it's the kind of joke she would like, and when that didn't work he quoted at her: "The Doctor said the universe was huge and ridiculous, and sometimes there were miracles. I could do with a ridiculous miracle about now..."