The Doctor, Amy, River and the Clerics have managed to get into the Byzantium but the Angels are close behind them. While they try to find a way out, Amy starts to count and nobody knows why she does it. They find the forest behind the secondary flight deck, which produces the oxygen for the ship. The Doctor talks to Angel Bob and find out through him that there is something in Amy's eye and that the Angels let her count to scare her. Soon the Weeping Angels have entered the flight deck when a crack appears in the wall that looks exactly like the crack in Amy's wall. With the Angels shortly distracted, everybody is able to flee into the forest but soon Amy feels bad and seems to die. The Doctor tells her, that there is an Angel in her head and it tries to come out but when she closes her eyes it freezes the Angel. He leaves her behind with some Clerics while he searches for the primary flight deck with River and Octavian. Octavian is caught by an Angel and tells the Doctor that River has killed someone and is in prison. Meanwhile, the crack comes closer and the Clerics who want to investigate it just vanish and Amy is alone in a forest with Angels surrounding her. Can the Doctor save her and does he trust River enough to help him?
The second part of this two-parter was somehow scarier because the Weeping Angels now look like real Angels. It's also the first episode where you can really see them move when they know that Amy can't see them, which looks really scary. In this episode we learn a bit more about the mysterious crack that first appeared in little Amy's wall. The Doctor finds out that it rewrites time and lets people forget about certain events or even persons. They just don't exist anymore because there is an explosion somewhere in time and space, that rips the whole universe apart. We also learn a bit more about River and that she is a prisoner because she killed someone. I guess it's a bit of a shock for the Doctor to hear this and he doesn't really know if he should trust her or not but she's River and you can't deny that there's a bond between them. "Flesh and Stone" is a really scary episode, which answers a couple of questions or at least gives you some hints. A great episode.