Charles II and some palace guards enter the King's daughter's room. He demands to know where the Doctor is. She is painting a nude portrait of the Doctor but feigns ignorance until a sneeze from beneath her skirts reveals the Doctor's whereabouts. Back in 2011, Amy reads aloud from a history book about "a mysterious doctor" who was put in the Tower of London on the order of the king and who escaped two days later, flying off in a magical sphere. She also recounts a break out from a prisoner of war camp in the Second World War that failed when the escape tunnel led to the commandant's office.

Amy wonders if the Doctor is just trying to get their attention. Rory, watching a Laurel and Hardy film, glances at the history book and misses the Doctor appear in the film and wave at the camera. An envelope is delivered, TARDIS-blue envelope, labelled with the number 3. Inside is a card with a map reference, date, and time. River Song receives an identical letter, but marked number 2, in her cell at the Stormcage Containment Facility. A guard warns his superior that she is packing her bags for a trip to a planet called America.

Rory and Amy arrive on a bus, getting out in the desert in Utah. The Doctor, wearing a Stetson, greets them excitedly. His hat is shot from his head by River. The quartet goes to a cafe where the Doctor and River compare diaries. The Doctor informs them that they are going to space in 1969.

Later, they have a picnic by a lake. The Doctor drops in the fact that he is over eleven hundred years old, some two hundred years older than when Amy and Rory last saw him. Amy sees a strange silhouette watching from the distance but when she looks away she forgets all about it. An old man arrives in a pickup truck and waves to them. Before he comes down to them an astronaut rises out of the lake. The Doctor tells the others not to interfere and walks down the beach to the astronaut. He tells the astronaut that it is alright, he knows who it is. The astronaut shoots the Doctor twice and he begins to regenerate, but a third shot kills him outright. The astronaut returns to the lake. River announces that the Doctor is dead. She shots at the departing astronaut but then says, to herself, "Of course not". The old man arrives as Amy hugs the dead Doctor. He has a can of gasoline. He says that he was invited by the Doctor who told him to bring the gasoline. He has an invitation marked number 4. He says that he is Canton Everett Delaware III. River explains that a Time Lord's body is a miracle; empires would value just one cell. Rory suggests using a moored boat for a Viking funeral and burns the Doctor's body. Delaware says he won't be seeing them again, but they will see him

River, Amy, and Rory go back to the cafe. Rory and River try to work out what the Doctor wanted them for though Amy is simply distraught that he is dead. Another invitation on a table, labelled number 1, leads them to speculate who the Doctor trusted the most. The Doctor comes into the restaurant, greeting them with delight. River slaps him but the Doctor appears not to know why. River asks how old he is and he tells them that he is nine hundred and nine. They realize the Doctor they saw die was a future version. River tells him that they have been hired by someone who trusts him to investigate space, 1969, and Canton Everett Delaware III.

In the TARDIS River tells Amy and Rory they cannot tell the Doctor of his death: his knowledge of it could rip a hole in the universe. The Doctor refuses to act on what they have told him of the mission because he knows they are hiding something. He asks River who she really is and who she killed. Amy convinces him to go with them by swearing on fish fingers and custard. The Doctor sets the TARDIS to "invisible" and "silent" (or, rather, River does so by readjusting the controls behind his back). He steps out of the TARDIS and finds himself in the Oval Office. President Richard Nixon is meeting with a young Canton Delaware. Nixon wants Canton to conduct an independent investigation. The young man has recently been thrown out of the FBI. He tells Canton about a child who phones him every night regardless of where he is. The child pleads for his help because the "space man" is coming to eat her. Nixon plays Canton a recording of a phone call, where the child appears to call herself Jefferson Adams Hamilton.

Nixon turns around to see the Doctor in the middle of the office. He calls security and agents enter the office, pointing pistols at the Doctor. He tells River to make the TARDIS blue again. His companions step out and are also held at gunpoint. When the claims to be an agent on loan from Scotland Yard, Canton, says that he trusts a man who can bring a big blue box into the Oval Office more than the man who let him do it. He tells him he has five minutes to solve the mystery. The Doctor asks for street maps of Florida.

Amy glances at the doorway of the office and sees a suited alien. She remembers seeing a similar alien at the lake but when she looks away she forgets it again. She says that she feels sick and is escorted to the women's toilet. The alien is waiting for her. A woman in the bathroom sees the alien, forgets it when she turns away, sees it again and disintegrated by it. Amy takes a picture of it with her camera phone. The alien tells Amy that she will tell the Doctor "what he must know, and what he must never know". Amy forgets the incident on leaving the room.

In the Oval Office, the Doctor finds what he has been looking for and enters the TARDIS with his companions and Canton. They materialize in a warehouse in Florida a few miles away from Cape Kennedy. Looking out of the window they see that Jefferson, Adams, and Hamilton are the names of three streets which intersect outside the warehouse. They explore the warehouse, the Doctor admitting that they have walked into a trap; River comments that the warehouse phone cords have been cut so the child couldn't have called Nixon from there.

They discover a large console, cables coated in slime and boxes of Apollo space equipment. River guesses Amy's plan to kill the astronaut to prevent it from killing the Doctor at the lake. She says that this would lead to a paradox.

River finds a hole in the floor down into a network of tunnels below the warehouse. She goes down and finds more aliens crouched in the shadows but forgets them as soon as she climbs back. She says that she wants to take another look. The Doctor sends Rory down with her. Rory finds a maintenance hatch. As she unpicks the lock, River tells him that when she and the Doctor first met, she was a young girl and the Doctor knew everything about her. River says that because the Doctor and she are travelling in opposite directions through time she will eventually meet a version of him that doesn't know her and that it will kill her. She opens the hatch. Inside is a console like the TARDIS.

Canton explains to Amy that he was kicked out of the FBI because he wanted to get married. They hear the little girl calling for help and run after her. Amy stumbles in pain while Canton runs ahead. The Doctor and Amy catch up with him further up the corridor. He is unconscious. Amy tells the Doctor that she is has something important that she needs to tell him: she is pregnant. The astronaut approaches down the corridor. Amy grabs Canton's gun. the astronaut lifts its visor: it is the little girl. Amy tells the Doctor that she is saving his life and shoots at the astronaut.

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.