To cut a long and tiresome story short, the Doctor invites Amy, Rory and River to come watch him die, but then the River from a different time refuses to kill him, which makes "all of history" happen at once. And by that they mean a few random things haphazardly thrown together. Winston Churchill is emperor of Rome, there are cars attached to hot air balloons for some reason, a Silurian is there, etc. and the Doctor tells Winston about what caused this state of affairs. This whole thing seems to be nothing more than an excuse to put Winston Churchill in the show again for some reason.
Then Amy shows up and kidnaps the Doctor, before revealing that she actually remembers him and is still on his side. Also Rory's there, being as bland and forgettable as ever. So they go meet River and eyepatch woman (who is their prisoner, along with a bunch of memory-wiping aliens), and now they've all got eyepatches like hers, because those are little computers that interface with your brain and store memories of the memory-wiping aliens so you can remember them, because they only wipe memories from living brains, not electrical devices. I actually thought that was pretty cool.
Anyway, River apparently knows that she's fucked up the universe by not killing the Doctor, and is such an incredibly selfish dickhead that she'd rather everyone in the universe die than that she have to kill the Doctor. It's worth pointing out that the Doctor is, in fact, in the universe, so she's killing him either way, and this way she also kills everyone else at the same time, but this doesn't seem to have occurred to her.
But before they can finish arguing about that, eyepatch lady reveals that by creating their own eyepatches they've fallen right into her trap, because the mindwipe-aliens can electrocute you with them. Except that this makes no sense at all. Firstly, why would she be willingly wearing a booby-trap like that. Secondly, when they reverse-engineered hers to figure out how to make more, why did they leave the booby-trap in? Thirdly, why is she still wearing hers? Why did they let her keep it? Fourthly, from the look of it, that's an awful lot of electricity zapping out of a device that interfaces directly with the brain; that seems like it should be way more deadly than it actually is.
All this is totally irrelevant anyway though as those guys want the exact same thing the Doctor wants, which is for River to stop being such a fucking retard and stop destroying the fucking universe (yeah, the "bad guys'" goal here is to prevent the universe from being destroyed). But they run away anyway and end up on the roof where River goes all melodramatic for a while. Then the Doctor marries her and whispers something to her and she finally agrees to stop destroying the universe and just kill him.
Except, big surprise, she didn't really kill him, he was actually a robot! Bet you never saw that coming! Well, actually I would have guessed he was a Flesh dopple. But no, he got the time-cop-torture-squad to give him their transforming robot, because people who go around torturing people are exactly the sort of people the Doctor has as friends. It's entirely consistent with the way he just murders fuckloads of people to make a point these days.
Earlier in the episode, Amy left eyepatch woman to die, and there was this whole thing about how th Doctor would never do that... except that he totally did do that, just then. He was right there in the room with them, and he didn't stop to help her. The writers seem to think that they can just tell you someone's good and nice and just and so on and that makes it true, no matter what their actions say.
But the worst bit is the ending, which seems t be hinting at an even more retarded story for next year. The great question of life, the universe and everything, the secret that they've been trying to kill him to protect? His fucking name. OK, maybe not his name, they have left it a bit vague, but honestly "Doctor who?" is the question? His identity isn't some huge secret. He just doesn't use his name because he's a renegade Time Lord, just like The Master, The Rani and several others. And the identities of non-renegade Time Lords were never any big deal. They just have names like Romanadvoratrelundar, Rassilon, Borusa or Spandrell. Time Lords are just people who happen to have time travel technology.
Well,. I guess it wasn't the worst season ending story, but considering the competition that's saying roughly nothing.