Three months have passed since the warehouse in Florida. Amy is running through the Valley of Gods in Utah. Her arms are full of tally marks in ink. Two vehicles chase her to a cliff where she halts. Several men step out, among them Canton Delaware. She asks if he remembers the warehouse but he responds by shooting her down.
In Area 51 the Doctor is tied to a chair inside a huge hangar. Armed guards watch him from a distance. Canton enters and throws down a photograph of Amy's arm. He asks the Doctor what the marks mean.
River Song is at the top of an unfinished skyscraper in New York City. Her body also shoes the tally marks. An alien confronts her and then she is cornered by FBI men. Canton tells her to surrender but she chooses to fall back out of the skyscraper and plunges towards the ground.
Rory, similarly covered in markings is cornered and shot at the Glen Canyon Dam. His body and Amy's are brought to the Doctor at Area 51. The FBI has spent three months building "a perfect prison" around the Doctor, made of dwarf star alloy. Canton seals himself inside with the Doctor, commenting that it is totally impervious to sound or radio waves. The Doctor, Amy, and Rory free themselves from their respective bindings. The invisible TARDIS is also in their prison and they step aboard. They travel to the side of the skyscraper as River falls and she plunges through the open door into the TARDIS swimming pool.
The three renegades reveal that the markings are a tally of how many aliens they have encountered in the past three months. The Doctor says that this is not an alien invasion, but an occupation.amy draws the Doctor aside and tells him that she is not pregnant after all. The Doctor takes them Cape Kennedy, where Apollo 11 is almost ready for launch. He tells them that the secret weapon to defeat the aliens is Neil Armstrong's foot.
The Doctor injects a device into his companions' hands that will record their encounters with aliens. It will flash to remind them of what they have seen. Canton leans over to adjust the Doctor's bowtie and then realises that his palm is flashing. There is a message in his voice telling him that he has just seen (and forgotten) an alien by the TARDIS doors. The Doctor says that it is a hologram derived from the image on Amy's phone camera. While Canton was looking at it the Doctor gave him the instruction to adjust his tie. As Canton forgot both the alien and the message, but acted on it anyway, the Doctor suggests that the aliens have been controlling humans with subliminal suggestion for thousands of years.
The Doctor tells Canton and Amy to start their search for the little girl by visiting children's homes, looking for anyone who has gone missing. Their trip eventually leads them to Graystark Hall, a children's home a few miles away from Cape Kennedy. The building is empty except for a rather disturbed warden. He thinks that the year is1967 and he is preparing to shut the home. There are messages painted across the walls telling him to leave but he says that the children (who left two years earlier) are painting them. He has similar messages on his wrist.
Amy goes upstairs and enters a room that appears to be empty. It is only when she notices that she has dozens of tally marks on her arms and face that she looks up to see a swarm of aliens hibernating on the ceiling. She exits, forgetting what she has seen instantly. As she moves down a corridor a hatch opens in one of the doors. A woman with an eye patch looks out and says that someone is only dreaming. Amy looks at the door again but the hatch has gone. She enters the room. It is a child's bedroom. There are toys and photographs of the little girl. One picture is of Amy with a baby. The little girl enters, wearing the astronaut suit, and asks for help. There is a bullet hole in the suit's helmet visor. Amy apologises for trying to shoot her. Two of the aliens follow the girl in and Amy screams.
Canton hears Amy's scream from the warden's office. An alien comes in and declares itself to be one of the owners of the planet. Shooting it three times, Canton welcomes it to America.
The Doctor is caught in the nose cone of Apollo 11 rearranging some of the electronics. He says he put it back exactly as he found it (apart from one wire). He is taken to a lecture theatre to be questioned by security but is rescued when River and Rory bring President Nixon to vouch for him. As they leave, Canton calls, requesting help.
They hurry to the orphanage. They enter the child's room. They can hear her but trace her voice to the nanorecorder, which has been taken from her palm. The Doctor says that it is broadcasting live. They also find the astronaut suit. The little girl is actually around the corner, listening to them speak. The warden arrives to say that someone has been shot. The Doctor goes to the office where the wounded alien is lying. The Doctor demands to know what it is and the creature says that it is the Silence and "silence will fall".
Canton takes the wounded alien to the Doctor's prison at Area 51. It is treated by a military doctor who promptly forgets all about it, repeatedly. The alien says that the Silence have ruled the world since the Stone Age. It adds that it was a mistake for Canton to have it treated; the humans should kill them all on sight. Canton records this speech on Amy's video phone.
River and the Doctor examine the space suit. They find it loaded with a dozen different kinds of alien technology to make it a perfect life support machine. They comment that the girl must be very strong if she could force her way out of it. River asks if the suit could move by itself, as this would explain the little girl's original phone call saying that a space man was coming to eat her. Rory listens to Amy's nanorecorder and hears her saying that her life was so boring before he "dropped out of the sky," and that she wants to see his "stupid face".
Amy recovers consciousness, tied to a machine in the console room and surrounded by the Silence. They tell her she has been there for several days.
On the day of the moon landing, the Doctor manages to trace the signal from Amy's nanorecorder. The TARDIS lands in the console room. The Doctor comments that it is like the one he saw in Aickman Road. He brings a television out of the TARDIS and tells the Silence that he is not a violent man but River would ki8ll at least three of them instantly if they attack. She ups the number to seven. He asks the Silence why the little girl is so important to them but they do not reply. The television shows a live broadcast of the moon landing. He uses the equipment he placed in the command module to insert a film clip of the video Canton took of the Silence saying that humans should kill them all on sight. He tells them that this will be one of the most watched pieces of film in human history and tells the Silence that it is time for them to leave. Around the world, people watching this broadcast begin to kill the Silence without thinking. The Silence begin to charge up their bodies to attack but River shoots them down in a dazzling display of marksmanship. Rory tries to free Amy, but she tells him to get his "stupid face" into the TARDIS. The Doctor frees her and everyone escapes into the TARDIS.
Canton is dropped back in the Oval Office. Nixon asks the Doctor how he will be remembered in the future and the Doctor says he will never be forgotten. He tells that Nixon should give his permission for Canton to get married and return to the FBI. Nixon asks if Canton's partner is black. Canton replies that he is.
The Doctor takes River back to the Stormcage Facility and offers her a chance to travel with him in the TARDIS but she says she has to serve her sentence in full. She kisses him passionately and is surprised to find that, for the Doctor, this is the first time. As he boards the TARDIS she reflects that, for her, it is the last.
The Doctor and Amy talk about her pregnancy. She says that she didn't tell Rory because she was afraid that her time in the TARDIS might give the baby a "time head'. Rory is listening to them speak on the nanorecorder. Amy is aware of this and tells him that she is not pregnant. The Doctor, however, scans Amy for pregnancy. The console display alternates between pregnant and not pregnant.
Six months later, the little girl staggers through a dark alley. She tells a concerned tramp that she is dying but says she can fix it. She begins to regenerate.