[Lord Nikon]

Predictable cliffhangar, as is the fact that next week's ep is the last one before the hiatus.
So far it looks like -

The silence is an evolved form of the flesh which has travelled back to try to take over the earth. That's when they took Amy, leaving a flesh replica for the current time, also why the Tardis had problems detecting her pregnancy.

Prediction for the season - River was in the spacesuit seen in the first episode and the doctor killed was a flesh replica.