The damaged TARDIS flies out of control above modern-day London, the newly-regenerated Doctor in his 11th incarnation clinging to the edge of the doorway. The Doctor manages to use his sonic screwdriver to trigger the controls, narrowly avoiding Big Ben. He finally manages to climb into the burning control room and close the doors, only to have the TARDIS shoot off in a different directions.
In the English village of Leadworth, 12-year-old Amelia "Amy" Pond is praying to Santa before going to bed and thanking him for everything. She comments about the crack on the wall, and insists that she hears voicing emerging from it. Amelia asks Santa for someone to come fix it. The girl hears a sudden thundering noise and a crash from outside, and goes to investigate. There is a smoking English police box in her garden, turned over on its side after smashing a shed. The doors burst open and a grappling hook flies out and snags. The soaking-wet Doctor climbs out and asks for an apple, insisting he loves them. She asks if he's okay and he explains that he had to climb up, and she wonders if he's a policeman who has come about the crack in the wall. The Doctor suddenly collapses but insists that he's fine as he clutches at his chest and exhales golden energy. When Amelia wonders who she is, the Doctor admits that he doesn't know and he's still cooking. He asks if the crack scares her, leaps to his feet, and goes to investigate... and promptly runs into a tree.
In Amelia's kitchen, the Doctor discovers that he doesn't like apples any more, or any of the other food he used to like in his previous body. He eventually settles for fish fingers and custard, and asks why she's in England. She explains that she's Scottish, and she lives with her aunt, who is out. When the Doctor wonders if Amelia is scared about being left alone, she says she isn't and the Doctor realizes she must really be scared of the crack. He examines it and realizes the crack doesn't go through the wall, but there's a draft. He scans it with his sonic screwdriver and explains that it's a crack in space/time, not in the wall itself. Amelia tells him that she hears voices occasionally, and he listens as a voice saying, "Prisoner Zero has escaped." He explains that there's a prison on the other side of the wall, and he needs to open it all the way to cause the forces to revert, closing it. Using his sonic screwdriver, the Doctor causes it to open, emitting a blast of energy. They hear the voice again, saying the same thing over and over. No one responds at first, and then a giant eyeball appears, looking at them. A burst of energy emerges, striking the Doctor, and the crack closes. The Doctor insists that everything is fine, He takes out his piece of psychic paper and discovers that it says the same message, "Prisoner Zero has escape."
The Doctor realizes that Prisoner Zero has escaped through the crack, and runs to search the house. He sees something in the corner of his eye and notices a door. Before he can investigate, the TARDIS cloister bell rings and the Doctor runs out to his vehicle, warning that the engine is going to explode. He says he needs to take it five minutes into the future to release the energy, and it's too dangerous to take her. When Amelia wonders if he'll be back, the Doctor promises that he'll return, jumps in, and dematerializes the TARDIS. Amy runs into the house and starts packing... unaware that the door the Doctor noticed is now open. She runs down to the garden and waits... and waits... and waits.
The TARDIS appears during the day, still smoking, and the Doctor emerges. There's no sign of Amy and he runs inside, shouting that he knows what the danger is and Prisoner Zero is there. As he turns, someone hits him in the head with a cricket bat, knocking him out.
At the hospital, Dr Ramsden comes in with the male nurse, Rory Williams. He informs her that all of the coma patients in the ward simultaneously screamed. She doesn't believe him, even though he explains that they called for her. One of the patients, Barney Collins starts chanting the word "Doctor," and then the others join in.
The Doctor wakes up and discovers a woman wearing a policewoman's uniform standing over him. She tells him to stand still, and he discovers she's handcuffed him to the radiator. The Doctor asks where Amy is and explains that since the engines were phasing, he went too far. The policewoman says that Amy hasn't lived there in six months, and the Doctor insists that he promised he'd be back in five minutes. As she apparently calls into the station, the Doctor notices the door.
Dr Ramsden examines the patients and discovers that they are all unconscious. Rory mentions the conversation he had with Dr Carver, and Ramsden insists that he couldn't have seen the patients walking around, but he insists he has photos. She still doesn't believe him and tells Rory to take some time off.
The Doctor asks to talk to whoever lives there, and asks how many rooms are there. When the policewoman wonders why, he says that it will change her life. She finally counts and says that there are five, but the Doctor notes that there are six. He tells her to look behind her out of the corner of her eye, and she sees the door to the sixth room. The Doctor explains that there's a perception filter in effect, and something came there to hide and she needs to uncuff him. The policewoman walks toward the door and says she lost the key, and goes inside despite his warnings. She finds nothing there, but the Doctor warns that it can affect her perceptions. He asks for her sonic screwdriver, and she notices that it's inside, lying on a table and covered in a sticky liquid. She reaches for it, unaware that a snakelike creature has dropped from the ceiling behind her. He tells her not to look out of the corner of her eye, because once it realizes she can see it, it'll kill her. She looks anyway and then runs out, giving the Doctor his sonic screwdriver.
The Doctor seals the door and then tries to free himself, but discovers that it isn't working. The door glows with energy and the Doctor tells her to run until her backup arrives. The woman admits that she didn't call for police backup. Her radio is a fake and she's a kissagram messenger. The door bursts open and Barney Collins and his dog emerge. The Doctor tells her to look at the faces. Barney and his dog start barking, and the Doctor explains that it's one creature disguised as two. He wonders where Prisoner Zero got the psychic link, and the alien snarls at him.
In the coma ward, Barney Collins remains unconscious.
Prisoner Zero opens its mouth, revealing huge fangs and something inside. However, the Doctor insists that they're not a threat because have backup. The woman admits they don't, and the Doctor then claims that they're harmless because they don't have pointless. The same voice as earlier announces that the residence is surrounded. Realizing they have backup, the Doctor explains it shouldn't harm them because they have backup. The alien voice orders Prisoner Zero to emerge or it will burn down the house. Prisoner Zero goes to the window while the Doctor finally activates his sonic screwdriver, frees himself, and runs out with the woman.
As they go outside, she explains that she pretended to be a policewoman because he broke into her house, and demands explanations. The Doctor gets to the TARDIS and tries to get it open, but realizes that it's rebuilding and won't let him in. He notices the nearby shed, which is twelve years older, and he realizes that he is twelve years late. The Doctor asks why she said it was only six months, and insists that it's important. She finally snaps at him and asks why he said five minutes, and he realizes that she's Amy, twelve years older. She grabs him and they run pass the house and into the village, where the alien voice continues to announce over an ice cream truck's radio that Prisoner Zero should surrender. The Doctor realizes that all the radios, cell phones, and MP3 players in town are playing the same message. He runs to a house belonging to Miss Angelo. Her TV has the giant eye on the screen and the same message repeating. The Doctor confirms that the message is broadcasting in every language, all across the world. He looks up at the sky and then figure that a starship will be arriving in 20 minutes. Both Miss Angelo and her grandson Jeff recognize the Doctor from the cartoons that Amy created of the "Raggedy Doctor." Meanwhile, the Doctor realizes that the aliens are referring to the entire planet, not just Amy's house.
Above Earth in orbit, dozens of ships hover as they issue their warning.
The Doctor determines where he is and realizes that there's no technology to help him. He spots a duck pond and notes that there are no ducks, and then clutches at his heart. He warns her that he's not ready. The sky grows dark and the Doctor explains that the aliens have sealed the planet in the force field. As people start taking photos, Amy wonders if it's all a joke. The Doctor suddenly remembers that he saw Prisoner Zero nearby, and Rory was taking photos of it. He then tells Amy that he can save the planet, and invites her along. Instead, Amy locks his tie in and asks how she can know who he really is. The Doctor shows her the apple he gave her and insists that he's a time traveler, and asks her to believe him for 20 minutes. Amy realizes that he's telling the truth and frees him.
The Doctor goes to find Rory, takes his cell phone, and asks why he's taking photos of Prisoner Zero instead of the darkened sky. Amy runs up and introduces Rory as a kind of boyfriend. He realizes that it's the Raggedy Doctor and he's real, and then explains that the man is a coma patient at the hospital. Prisoner Zero appears behind them as the alien spaceship appears above, scanning the village. The Doctor realizes it's scanning for an alien presence and uses his sonic screwdriver on full power to attract its attention. It burns out and the alien spaceship flies away without noticing. Prisoner Zero desolidifies and flows down into the sewers. The Doctor explains that they have to drive it out into the open, but he only has 17 minutes and no TARDIS or sonic screwdriver.
Dr Ramsden tries to wake up Barney, while Prisoner Zero emerges from a nearby vent and snarls.
The Doctor explains that the aliens noticed him through the crack, got a fix on him while looking for Prisoner Zero, and eventually got to Earth 12 years later. He takes Rory's camera and determines that Prisoner Zero has been assuming the form of the patients and walking around the village. The Doctor sends Rory and Amy to the hospital while he goes to see Jeff, who has a laptop. He uses it to hack into a conference call of experts, including Patrick Moore. The Doctor gives them several unique scientific formulas to prove that he's a genius, and then tells them to pay attention.
Amy and Rory arrive at the hospital.
The Doctor writes a computer virus in a phone and sends it to all of their computers, and explains that it will reset every counter it can find on cameras, computers, etc., at exactly the same time. He then tells Jeff to explain why they can trust him, and tells him that he will be famous in ten minutes. However, right now he has to get them to trust him, because today is the day he saves the world. The Doctor then runs off while Jeff talks to the experts;
At the hospital, Amy calls the Doctor to warn him that they can't get through. He's stolen a fire truck to get to the hospital, and tells Amy to go in posing as a policewoman. In the ward, they find a mother and her two daughters. She says that something killed Ramsden and all the nurses, but she and the children all talk in chorus and Amy realizes that it's Prisoner Zero. The three individuals all bare their fangs and scream, and Amy and Rory barricade themselves in the coma ward. She informs the Doctor what's going on, and he asks what window is nearby. Prisoner Zero bursts in and says that it watched as she waited 12 years for her magic Doctor to appear. The Doctor sends a text message, "Duck," and them smashes the fire truck ladder in through the window and climbs in. He says that they still have enough time. Prisoner Zero says that the Atraxi will find her, so she plans to die in flames. When the Doctor suggests she go back through the crack, Prisoner Zero explains that the cracks originated elsewhere, and realizes that the Doctor doesn't know where the cracks came from. It taunts the Doctor, and warns that, "The Pandorica will open, and silence will fall.
The Doctor suddenly points out that the clock in the ward has reset to 0:00. Across the world, every counter has set itself to zero, and the Atraxi will track the computer virus to its source: Rory's cell phone, in the Doctor's hand. The Atraxi scan the hospital, but Prisoner Zero warns that they can't sense it while it's in human form. The Doctor explains that the camera has the photos of all of the bodies she duplicated. He uploads the photos to the Atraxi, but Prisoner Zero says it will take on a new form. The Doctor warns that it will take years to form that kind of psychic link, but Prisoner Zero says it's had years. Amy collapses and Prisoner Zero takes on the form of the Doctor from her memories. "Amelia" appears and explains that it took on Amy's memories, and the Doctor dreamed about her. The Doctor realizes that Amy is dreaming about him, and tells her to dream about what she saw: Prisoner Zero in its original form. Prisoner Zero impersonates itself, and the Atraxi detect and restrain it. It fades away, warning the Doctor that "silence will fall."
The force field disappears and Amy wakes up. The Doctor calls the Atraxi and tells them that they violated the Shadow Proclamations. He tells them to return and then goes to find new undamaged clothing. The Doctor then steps out on the roof, tries on ties, and tells the Atraxi that Earth is important and they should leave and never return. He points out that the world is no threat to the Atraxi. They scan and confirm that Earth is harmless, and the residents are guilty of no crime. The Doctor then points out that other aliens have come to Earth... and he's the one who stopped them all. He tells the Atraxi to run, and they quickly leave.
The TARDIS key glows and the Doctor realizes that it has finished rebuilding. He slips away and runs to Amy's garden, where the TARDIS is waiting in a slightly different form. He opens the door and stares in wonder. He goes in and departs as Amy and Rory arrive and watch his departure. Amy closes her eyes, and remembers waiting for the Doctor.
Later, Amy wakes up to the sound of the TARDIS materializing in her garden. She goes outside as he apologizes for leaving to run the TARDIS up to the Moon on a test flight. The Doctor invites her to come along and travel with him, wherever she likes. However, she explains that it was two years since he left. The Doctor insists that she's waited long enough, but Amy says she grew up. He assures her that he'll fix that, snaps his fingers, and the TARDIS doors open. They go inside and the Doctor shows her the newly rebuilt TARDIS console room. She wonder why he's so sure that she'll come along, and he figures she's been a Scottish girl in an English village, and has kept her accent. She asks if he can get her back the next day, and the Doctor assures her that he can and wonders what she has to return for. Amy insists that it's just "stuff." Amy wonders why he wants her to come along, and he promises that it's only because he's lonely. The Doctor assures her she isn't imagining things, and departs in the TARDIS with his new companion.
Left behind in Amy's house are all the toys and cartoons she made of herself and the Raggedy Doctor... and a wedding dress.