Two months have passed-Amy and Rory are enjoying their marriage, on a break from travelling with the Doctor. Eventually, they, as well as River Song, are sent letters-in TARDIS blue envelopes-summoning them to Utah. The group enjoys a picnic at a nearby lake, when suddenly, a strange astronaut arises from the water.
And shoots the Doctor dead.
A man then arrives with gasoline, telling them that the Doctor is definitely dead, and they give him a Viking style funeral. Canton says they’ll meet again, although he personally won’t…
Amy, River and Rory convene in a local diner, only to be incredibly shocked when the Doctor emerges from the restroom. Initially thinking he faked his death, they then realize that this is a younger Doctor, from a time before he got shot.
Turns out he got an envelope too, from his future self, but the companions choose not to reveal that he’s going to die in the future. The group decide to go back to 1969 and meet a younger Delaware, who is in the FBI and working with President Nixon. Turns out Nixon has been receiving phone calls from a frightened young girl. Working with Nixon and Delaware, the group locate the signal.
However, meanwhile Amy, using the restroom, encounters a strange alien being called the Silence, which have the ability to make people forget about them if they’re not looking directly at them, and who are also able to create post-hypnotic suggestions.
Eventually reaching a warehouse, they discover a TARDIS style ship similar to the one above Craig’s apartment from last season. They also encounter the Astronaut again, with the face revealing a young girl. Also Amy tells the Doctor she’s pregnant.
Escaping the warehouse, the group then begin to track the silence and the girl, using gadgets and marking their skin to tally the amount of times they’ve encountered the aliens. She also tells the Doctor that she’s not really pregnant. Amy and Canton are able to link her to a local mostly abandoned orphanage, where she is being kept by the Silence. At the orphanage, among the girl’s photos, is a picture of Amy with a baby. Amy is then captured by the Silence.
However, the Doctor, Rory and River are able to rescue Amy, and also defeat the Silence by turning their own post-hypnotic message against them embedded in the moon landing, as a captured Silence stated that they should be all killed on site. The astronaut girl is able to escape. Bidding farewell to Nixon, and returning River Song to her prison, The Doctor wonders about Amy being pregnant. He does a passive scan of her, and the results are very confusing, as they’re reading both positive and negative.
Meanwhile, back in the 60s, the astronaut girl, now sick and dying, shows up in New York. However, she doesn’t die…but begins a regeneration.