We found out the answers to some of the questions asked last week, but by no means all. We know who the Silence are and what they want, but the question of whether Amy can save the Doctor is another matter. It seems that Amy and Rory had left the Tardis because Amy was pregnant, but she hadn't told Rory because she was worried about what effect being conceived in the Tardis would have on the baby. However, it seems that at some point in the three months between the two episodes she was captured by The Silence and taken back in time a few years. While captive, she gave birth and her daughter was brought up in the creepy orphanage. I don't think she was in the astronaut suit when it assasinated The Doctor, though. The Doctor's plan to defeat the Silence, while a classic Hoist By Their Own Petard (The Avengers used to be particularly fond of that tactic) was one of the most chillingly ruthless things I've seen him do. The assasination at the beginning of The Impossible Astronaut was probably The Silence's revenge. Still don't know why they were trying to blow up the Universe last season though.
My favourite bit, however, was this conversation between The Doctor and Rory.
This is their empire. It would be like kicking the Romans out of Rome.
I know. I was there.
So was I.
The Doctor's already got everything in place for his plan at this point, but he's turning to Rory for reassurance before going through with it. I often think that Rory is the bravest of the current Tardis crew - The Doctor's used to a life of adventure, and Amy enjoys the danger - in Flesh and Stone it appears that she enjoys it a little too much.
There's a big surprise at the end - it turns out that Amy was right that being conceived in the Tardis might have affected her baby. It's apparently turned her into a Time Lord.