Three Months Later – July 1969
In the Valley of the Gods in Utah, FBI agents led by Canton Delaware pursue Amy through the desert. They corner her at the end of a cliff and Canton has one of his men roll out an empty body bag. He draws a gun on her and prepares to shoot, and she asks if he can remember why he’s ready to kill her. She reminds him of the warehouse, but Canton shoots her down. As Amy collapses, black hash marks on her skin are visible.
Area 51 – Nevada
Canton goes to a hangar where the Doctor is held under the most secure conditions possible. Canton asks the Doctor about the marks on Amy’s skin, and the Doctor realizes that the photos were taken of Amy’s corpse.
River Song is in the top floor of a skyscraper under construction, wearing a party dress and scanning similar hash marks on her arm. She hears someone approaching and retreats to the window, and finds the business suited-aliens closing in on her. River tells them that she sees them and makes more marks on her skin. Canton and his agents arrive and call out to her, and River turns her back on the aliens. When she turns back, they’ve disappeared. River runs to the open window and tries to tell Canton that they are everywhere, and America is being invaded. He humors her and then says that she’s coming with them, and River smiles and falls backward out the window.
Canton returns to Area 51 as scientists start to brick the Doctor in using zero-balance dwarf star alloy. The agent tells the Doctor that River killed herself, but the Doctor realizes that they’re building him a prison and warns that it still won’t be enough.
Glen Canyon Dam – Arizona
Rory, covered in hash marks, emerges onto the top of the dam as FBI agents close in on him. Canton says it would look better if Rory ran, and then shoots him down anyway. He then takes Amy’s and Rory’s corpse to Area 51 and puts them next to the Doctor, where the dwarf-alloy cell is complete. Canton seals the cell and assures the Doctor that nothing can get in or out. The Doctor immediately frees himself and Rory and Amy reveal that they’re alive. The Doctor uncloaks the TARDIS and the four of them enter. They open all the doors to the swimming pool.
River falls into the TARDIS doors as it rests on the side of the building, and falls into the swimming pool. As she dries off in the console room, the Doctor says that no one remembers the aliens but they’ve been on Earth a long time. He pilots the TARDIS to Cape Canaveral in Florida and tells them that they have a secret weapon: Neil Armstrong, aboard Apollo 11.
At the Graystark Hall Orphanage, Canton and Amy arrive in a car and they check their hands.
Earlier in the TARDIS, the Doctor and his friends review. It’s been three months since the incident at the warehouse, and they’ve learned that the aliens are in every country in the world, with a greater concentration in America. The Doctor gives them injections on their palms, and then secretly checks with Amy, who says that she wasn’t pregnant after all. River reminds Canton that he has seen the aliens as well, and they can’t remember them because the aliens edit them out of the viewers’ memory once no one sees them. They mark their skins to remind themselves that they’ve had an encounter. The Doctor warns them that they’re leading a revolution, and the battle begins today. He then explains that he’s been injecting them with a nano-recorder. It establishes a telepathic connection and records them logging any encounters with the aliens so they can play them back when the light flash.
Everyone stares at Canton as he adjusts the Doctor’s tie, and he realizes his hand is flashing. He plays the recording and listens to his own voice and the Doctor’s, saying that one of the aliens is in the TARDIS and that Canton should adjust the Doctor’s tie and then turn around. Canton turns around and sees one of the aliens in the TARDIS. The Doctor explains that it’s a hologram extrapolated from the image on Amy’s phone, and asks Canton to describe it. None of them can describe it, and they realize that the Doctor has implanted a hypnotic suggestion just as the aliens do to make them forget. Next, the Doctor tries to work out how the little girl is involved and where the aliens procured her. He tells them to check children’s homes to see which one is missing a little girl while he goes to NASA.
Now, Amy and Canton talk to the head of the orphanage, Doctor Renfrew. He invites them in and they see writing on the walls, messages telling the reader to get out while they can. Renfrew apologizes, explaining that it keeps appearing. Renfrew is vague as to who is doing it. He takes them to his office and Canton notes that the orphanage was closed in 1967. When the FBI agent tells Renfrew that it’s now 1969, Renfrew has no idea that two years have passed. Amy goes to check upstairs while Canton goes with Renfrew. She finds empty rooms and more written messages, and calls the Doctor. He tells her to find out what she can but not to hang around. The Doctor than hangs up and completes his work on the Apollo 11 command module, leaving a new unit inside. The authorities arrive and arrest him.
The door to the room closes behind Amy. As she runs to open it, she notices that her nano-recorder is flashing and plays it back. It is her own voice, saying that they seem to be asleep and that she should get out. As Amy tries to find a way out, she notices more hash marks on her hands and face. Turning, Amy sees dozens of the aliens hanging from the ceiling, asleep. She carefully makes her way to the door but bumps a wastebasket. They start to stir and she makes another entry… and the aliens disappear and the door opens. Stripped of her memories, Amy leaves, unaware that the aliens are watching her.
The NASA head of security, Gardner, interrogates the Doctor, who insists that he’s on a mission for President Nixon. Right on cue, Nixon arrives with River and Rory as his assistants. Nixon thanks Gardner for his services and chats with Grant, and then confirms that the Doctor is working for him. Gardner quickly gives in and releases the Doctor, and they all leave via the TARDIS
Canton asks Renfrew what he’s been doing, and the doctor says that “they” told him to make sure the child is protected.
Amy finds a woman with an eye patch, locked up in a cell and looking out the viewing slot. The woman talks to herself, saying that Amy must be dreaming, and then closes the slot. Amy discovers that the door is unlocked and opens it, and is surprised to see that the slot has vanished. Inside is a children’s room but no sign of the woman. There are photos of the girl on the dresser, including one of Amy holding the girl as a baby. Hearing a sound behind her, Amy turns and finds herself facing the astronaut. She asks who it is, and the spaceman opens the visor of her helmet. It’s the little girl, and Amy apologizes for trying to shoot her earlier. She explains that the little girl will kill the Doctor in the future, and the little girl begs her for help. The aliens come in behind her and Amy screams in terror as the door closes.
Renfrew hears a knock on the door, opens it, and then turns back. Canton asks who it was, and Renfrew has no memory of who it was. One of the aliens comes in and Canton tries to communicate with it by activating his nano-recorder. It doesn’t respond at first, and Canton hears Amy calling for help. The alien finally tells Canton that Earth is theirs and they have no need of weapons. Canton draws his gun and shoots it and runs to find Amy.
In the Oval Office, the Doctor tells Nixon to record everything in the office and asks the President to trust him and no one else. River tells the Doctor that Canton needs them and they depart in the TARDIS.
Canton searches the orphanage and follows Amy’s voice to the cell. The door is locked and he starts to shoot it open, but the Doctor, Rory, and River arrive. The Doctor opens the door with his sonic screwdriver and they go inside, unaware that the little girl is down the hall, hiding. There’s no sign of Amy in the cell, but they find an empty spacesuit and Amy’s nano-recorder on the floor. It’s playing Amy’s voice, begging for help, and they wonder how they can still hear her. The Doctor confirms that it’s a live transmission, but it’s one-way. Amy calls to the Doctor, asking him to rescue her, and Rory vows to bring him.
Renfrew comes to the door and says someone has been shot and they need to help. However, he can’t remember who needs help. They go to his office where the alien is on the floor, injured. The Doctor approaches it and asks who it is, and it says that they are The Silence. As it says that “The Silence will fall,” the Doctor remembers the previous times when he’s heard of The Silence.
At Area 51, the dwarf-star cell opens and Canton emerges. When the sergeant on guard insists that he talk to Colonel Jefferson, Nixon emerges and tells the soldiers to stand down.
At the Florida warehouse, River and the Doctor examine the spacesuit and find it filled with alien technology. The suit can sustain the wearer indefinitely, weaponry that can be fired by remote, and systems capable of hacking into any communication system, including the President’s phone. The system defaults to the highest authority it can find, so when the little girl became scared, she was connected to the most powerful man on Earth. The Doctor examines the TARDIS-blue envelope that he received and River says that he won’t find out anything by examining it. He asks River for more information, but she reminds him that they encounter each other in reverse. River confirms that the little girl forced her way out of the suit, and the Doctor believes that the girl will find them. As they work, they watch the broadcast of the Apollo 11 launch. The Doctor speculates that The Silence has infiltrated humanity for millennia, and wonders why Mankind is suddenly launching a ship to the Moon.
Canton calls in Dr. Shepherd to examine The Silence alien and wonders who has been treating it. The FBI agent notes that Shepherd has already treated it and forgotten, and Shepherd goes to report it to his superior... and forgets as soon as he looks away. Once he leaves, The Silence warns Canton that he was foolish to tend to his wounds. The FBI agent records video of it on a borrowed mobile phone as it vows that Canton will soon forget, and then sends the recording to the Doctor in Florida.
Meanwhile, the suit activates by itself, and River suggests that the spacesuit was coming to “eat” the little girl, just as she warned. Meanwhile, Rory listens to Amy’s transmission of her saying that she loves him. He asks the Doctor why he hasn’t traced the signal, and the Doctor explains that he’s not sure what to do since The Silence basically control the planet. He then asks Rory if he remembers the two thousand years waiting for Amy. Rory admits that he only remembers some of it, and tries not to.
Across the world, people watch for the next eleven days as Apollo 11 comes in for a landing on the Moon.
Amy finds herself on a table in the underground control chamber, surrounded by The Silence. They identify her by name and say that they do her honor. When they tell her that she will bring The Silence, but her part will soon be over, Amy warns them that they’ve made a mistake and the Doctor will soon come for them. However, she’s shocked when they explain that she has been there for many days and has forgotten. As it starts to lean over her and tells her to sleep, the TARDIS appears in the chamber and the Doctor emerges. He recognizes it from the flat in London and tells Rory and River to keep their eyes on The Silence at all times. The Doctor then brings out a television and turns it on, and warns them that if they attack, River will shoot at least the first few of them. He asks them to surrender and promises to let them go, and then says that it won’t be that easy for them. When The Silence says nothing, the Doctor asks who the girl is and why she is important, but still gets no response.
The Doctor informs The Silence that half a billion people are watching the landing, the first step in Mankind spreading out across the stars. He explains that everyone watching will never, ever forget Neil Armstrong stepping onto the lunar surface, and then calls Canton, who is in the dwarf-star cell. Canton broadcasts the video of his alien saying that they should kill them. In a hypnotic trance because of the sight of the alien, every human on Earth turns on the aliens in their midst. The Doctor tells The Silence that they are no longer safe on Earth, and humans will wipe them out without ever remembering. The Silence starts to fire energy blasts and River opens fire on them. Rory is unable to free Amy, but promises never to leave her. She tells him to get his stupid face out of there and Rory hesitates, and the Doctor releases her. As Rory gets Amy into the TARDIS, The Doctor waves his sonic screwdriver around and River points out that he’s not helping, and tells him to get into the TARDIS while she dispatches the remaining Silence.
As the Doctor and River pilot the TARDIS away, Rory points out that Amy said he has a stupid face. He admits that he wasn’t sure who she was calling on to rescue him, and Amy assures Rory that it was him she wanted.
The Doctor goes to the Oval Office and Nixon thanks him for his help. However, the Doctor warns that there are billions of things out there just waiting. He then tells Nixon that Canton wants to get married, and the President assures him that something can be arranged. Nixon asks about his own future and if he’ll be remembered, and the Doctor assures him that they’ll never forget him. As he leaves, Nixon asks Canton about his intended spouse, and Canton says that it’s a black man. The President says they should go slowly.
The Doctor drops River off at her cell and suggests that she could go with him, but she says she can easily escape and has a promise to live up to. He starts to walk away and River calls him back long enough to kiss him. Shocked, the Doctor points out that they’ve never done it before, much to her surprise. He quickly leaves, and she realizes that it’s the last time for her just as it’s the first time for him.
Once he’s alone with Amy, the Doctor asks her if she’s okay. She admits that there are some things she can’t quite remember, unaware that she has forgotten the photos of her holding the little girl. The Doctor asks why she said she was pregnant, and why she told him. Amy says that he’s her best friend and he asks why she didn’t tell Rory. She explains that she was worried that traveling in the TARDIS may have mutated the fetus. Rory has been listening to them via the nano-receiver and steps out, and insists that she should have told him. Amy hugs him and Rory is reassured. The Doctor wonders if they should check on the little girl, but decides to go off an adventure instead. However, he secretly checks via the TARDIS scanners but is surprised when it can’t tell if she’s pregnant or not.
New York, 6 months later
A tramp is in an alleyway rummaging for food when he sees the little girl, coughing. She tells him that she’s dying but she can fix that. Her hands glow with golden regenerative energy as the tramp runs away, terrified.