OK, if you haven’t already seen these episodes, you might want to look away now, because here be spoilers. I’m not exactly going to run through the whole storyline, but I am going to drift around it and refer to some details. And as some of this inevitably ties into A Good Man Goes To War, if you haven’t seen that yet you may want to leave this post until later.
Right, I’m assuming that if you’re reading this bit, you’re really ready.
First, let’s backtrack a bit. The key to what’s going on in this is Amy’s ShrÃ¶dinger pregnancy, which the TARDIS scanner kept showing as there and not there. And it seems the Doctor, not for the first time, knows a lot more about what’s going on that he lets on to his friends, which means that when the TARDIS arrives at an old monastery now being used as an acid mine, it’s neither accidental nor coincidental. Because the mine is an early stage in the use of something called The Flesh. The Flesh is a semi living material that can take on the form of any living tissue, and can be remotely operated by a person from a safe distance. The operator reamins safe, and apparently unconscious while experiencing things from the Flesh avatar. All very nice until it goes a bit wrong, as things generally do.
And what goes wrong is that the Flesh copies of the acid mining crew become self-aware and adopt a life distinct from their originals. And they’re not at all happy. They remember being dissolved back into the mass of Flesh time after time. They get even less happy when it turns out that the humans have been discarding faulty Flesh copies in the cellars, and that those copies are aware…
So far, so base under seige/rebellious robot. But it gets more interesting when the Flesh produces a copy of the Doctor, who after a bit of confusion (jelly babies, neutron flows, etc) settles down to being as much the Doctor as the Doctor.
It all gets a bit like The Thing towards the end, when one of the Flesh copies goes a bit loopy and turns into a quite nasty form. But humanity comes through, and the other Flesh copies realise that they need to work things out and get along better with the human humans.
All of which would have been a nicely entertaining, good bit of fun and well worth being a two-parter. But that was far from the end.
Back in the TARDIS, the Doctor reveals what he’s known. The Amy that’s been around since The Impossible Astronaut isn’t Amy at all. Those views of the strange woman with an eyepatch are reality breaking through. Amy is being held somewhere, and she’s been replaced by a Flesh copy. Rory’s a bit upset about that, as well he might be.
The real Amy really is very pregnant, and about to give birth. After promising to fakeAmy that he and Rory will come and rescue her, he zaps her with the old sonic, which reduces her to the white gloop that is the normal form of the Flesh.
And that’s all a wee bit confusing, isn’t it? Amy was presumably captured at some off-screen point and replaced with a duplicate which contained (for lack of a better word) her consciousness and awareness, which is some pretty clever going since it means that however it was done involved projecting a two-way communication channel into the TARDIS wherever it happened to be in time, space, outside the universe as we know it, and in the Time Vortex. And whoever has done that seems to have done it with the intention of taking hold of Amy and Rory’s baby.
Why? How? When? Who? At least some of those questions will be answered in A Good Man Goes To War. But not all of them. That would be silly.
 Yes, apparently in the future, acid bubbles up from the ground and gets collected in industrial processes