There is a house with an overgrown and neglected garden. A weather-beaten house stands quiet in the night. It is the year 1996, Easter, and, in her bedroom, Amelia Pond is praying to Santa for help with the large scary crack in her bedroom wall. Her Aunt Sharon has told her that it is an ordinary crack but Amelia knows otherwise: at night there are voices. She asks Santa to send someone to fix it, or a policeman. Seconds later there is a crash in the garden outside. She runs to her window and sees a police box, belching smoke, lying in her garden. It has smashed the garden shed. She looks up at the sky and says, "Thank you Santa".
She runs down and as she gets to the box the doors burst open and a grappling hook flies out. The Doctor climbs out, soaking wet. He immediately asks for an apple, all that he can think about. He explains that he was in the library, as was the swimming pool. She asks him if he is a policeman who has come about the crack in her wall. He collapses to his knees and breathes out a golden smoke. He asks her if the crack is scary, and then introduces himself as the Doctor. He tells her not to ask stupid questions and not to wander off. He then promptly walks into a tree. Apparently suffering from some post-regenerative disorientation, he demands that she give him an apple which he spits out in disgust. Following this he requests other foods and rejects each in turn. These include yoghurt ("Stuff with bits in"), bacon ("Are you trying to poison me?"), baked beans ("beans are evil. Bad, bad beans") and bread and butter (which he throws out into the garden). Finally, he searches through the fridge and finds some fish fingers which he dips into a bowl of custard. When she tells him that her name is Amelia Pond he says that it is brilliant, like a name in a fairy tale. She adds that she doesn't have a mum and dad, just an aunt.
The Doctor asks Amelia to show him the crack in her wall. As he looks at it Amelia hands him an apple with a smiley face gouged out of the skin. Then, he hears a voice on the other side saying that Prisoner Zero has escaped. He suspects that the crack is connecting Amelia's room to another dimension (the crack would still be there if the wall wasn't) and tries to close it with his screwdriver. In order to do this he has to open it first. As he does so a large eyeball peers through. It shoots a particle of light at the Doctor and the crack closes again. The Atraxi (the prison guards on the other side) repeat that Prisoner Zero has escaped. The Doctor thinks that the prisoner may have come through the crack. While he is exploring the upper floor of the house he begins to suspect that all is not as it seems but is distracted by the sound of the cloister bell in the TARDIS. He tells Amelia that the engines of his time machine are phasing he needs to take his ship on a short trip to stabilise it but he will return for her in five minutes. She says that people always say that they will come back but never do. He tells her to trust him, he is the Doctor.
As he dematerialises she returns to her room to pack her case. She has not seen a door opening on the landing of the house. She waits for him in the garden but he does not come back that night.
The TARDIS lands in daylight and the Doctor rushes out to find Amelia; he has realised what he missed earlier. He sonics the door, telling her she has to get out of there. He runs up to the landing and is felled by a blow from a cricket bat.
In a coma ward of a nearby hospital a nurse brings Dr Ramsden to hear the patients calling out, "Doctor!" she is perplexed but the nurse adds that he has seen the patients wandering around the village. She tells him he needs to take some time off, starting now.
When the Doctor recovers consciousness he sees a tall, attractive policewoman standing over him. He asks her where Amelia is and she tells him that the little girl has not lived there for six months. He refuses to believe that he is six months late - he promised her five minutes. She says that she has radioed for backup which will be there shortly. The Doctor realises that he is handcuffed to a radiator. He asks the policewoman to count the doors on the landing. She does so: there are five. He tells her that she is wrong, there is a sixth door hidden by apperception filter.
The policewoman goes to investigate this new room despite the Doctor telling her that it is very dangerous. She finds herself in a bare, dusty room. The Doctor's sonic screwdriver rolled into the room under the door when she attacked him but now it is lying on a table and is covered in slime. Prisoner Zero, a long serpent-like creature with needle teeth steals up behind her. She turns, sees it and flees back to the Doctor. He uses his screwdriver to shut the door but the door bursts open and a man and a dog emerge. The Doctor realises that this must be the prisoner, an inter-dimensional multiform, when the man begins to bark. The man opens mouth to reveal razor sharp teeth.
The Doctor tells Prisoner Zero that police backup is on the way but the policewoman tells him that this is a bluff: her radio is a fake and her police outfit is just a kissogram costume. The Atraxi voice is heard again saying, "Attention Prisoner Zero. The human residence is surrounded. Prisoner Zero will vacate the human residence or the human residence will be incinerated."
The Doctor frees himself and he and the woman run out to the TARDIS but the key will not open the lock on the door and entry is impossible. The Doctor says that the TARDIS is still repairing itself. He notices that there is a new shed to replace the one he crashed into. After licking it he announces that it has been there for twelve years. He asks the woman why she said six months and she responds by asking why he said five minutes, thus revealing herself to be Amelia. Prisoner Zero, in the shape of the man and dog, exits the house. Both man and dog are barking.
As they stride through the village streets Amelia says that the Doctor is twelve years and four psychiatrists late; she kept biting them because they said he wasn't real. They hear the Atraxi warning coming from an ice-cream van's speakers. The Doctor realises that the warning is being broadcast to the world and that the residence in question is not Amelia's house but the planet
The Doctor and Amelia enter the house of her friend Jeremy. Both he and his grandmother call the woman "Amy'. The grandmother seems puzzled that Amy is now a policewoman and not a nurse or a nun. They also recognise the Doctor as a character called "The Raggedy Doctor" from little Amelia's childhood. A big blue eye on the television screen is repeating the warning. Out in space a fleet of space ships orbit the Earth.
The Doctor and Amy go out into the middle of the village. He tells her that the Atraxi are going to put a force field around the planet and incinerate the atmosphere. On the village green there are a number of people taking photographs of the sun as it vanishes in the sky. The Doctor tells Amy that he has about twenty minutes to save the planet. He tells her she can help him or go home to be with her loved ones. Instead, she traps him by slamming a car door on his tie and demands to know who he is. He produces the apple that she gave him as a child twelve years earlier. He asks her to believe in him for just twenty minutes. This gains her trust and she frees him.
One person attracts the Doctor's attention because he is photographing somebody else: a man walking his dog. The Doctor is drawn to this man, a nurse from the hospital. He is Rory Williams, Amy's boyfriend. The Doctor takes Rory's phone and asks what he was doing. Rory tells him that he has been seeing people walking around the village that he knows to be in comas in the hospital. The Doctor accosts Prisoner Zero and says that the Atraxi have been drawn to the planet by the presence of alien technology. A star ship passes overhead, scanning. He says that he will attract their ships, seen searching the planet, by using his screwdriver. He lets off a sonic burst that shatters lights and windows as well as setting vehicles in motion. Unfortunately, the screwdriver explodes in his hand. The Atraxi ships move off and Prisoner Zero disappears down a grid. The Doctor says that he has to drive Prisoner Zero into the open.
The Doctor tells Rory and Amy to go to the hospital to investigate and empty the coma patients from the ward. Prisoner Zero arrives first and attacks the doctor on the ward.
The Doctor heads back to Jeff's house and finds him in his bedroom using his laptop. The Doctor is horrified by what Jeff is looking at and tells him to 'get a girlfriend.' He then uses the computer to call a conference of various scientific figures including NASA, Jodrell Bank, Tokyo Space Centre and Patrick Moore. He feels it necessary to prove his credentials by giving them the solution to Fermat's Last Theorem and FTL travel. Once he has secured their attention he uses Rory's phone on which he creates a virus that he tells the scientists to spread around the world. He leaves Jeff in charge of convincing the scientists to believe in him. He tells him that this is the day he saves the world. He also adds that Jeff might want to delete his internet browsing history.
Amy's police costume allows her to gain entry to the hospital which has been sealed off from the public. She and Rory head to the coma ward where they are met by a woman and her two daughters. She says that the doctor and the nurses are dead. It is apparent when the wrong voice comes from their mouths that this is Prisoner Zero. Amy phones the Doctor to tell him what has happened. He is already on his way, driving a fire truck. He sends Amy a text that tells them to duck as the ladders on top of the truck smash through the window. The Doctor climbs into the ward. He tells Prisoner Zero to reveal its true form to the Atraxi but it refuses. He then says it can open another crack in order to escape but it taunts him because "The Doctor in the TARDIS doesn't know' where the cracks came from. It adds a strange prophecy that "The Pandorica will open. Silence will fall".
The Doctor's virus takes effect, turning all of the world's digital displays to zero. The Doctor tells Prisoner Zero that this will alert the Atraxi to this source: Rory's phone from which he has also sent all of Rory's photographs of the various coma patients. An Atraxi ship hovers above the hospital.
Prisoner Zero says that, after all of its years hiding in her house, it has formed a link with Amy. It changes shape so that it now resembles the Doctor holding little Amelia's hand. It says that Amy is dreaming about the Doctor. The Doctor manages to make Amy, now unconscious on the floor, dream of the Atraxi's true form as she saw it in the room in her house. Before Prisoner Zero can physically attack the Doctor it is caught in the Atraxi's energy beam. It disappears.
Amy recovers consciousness. The Doctor tells the Atraxi not to leave the planet. He calls them back, invoking the rules of the Shadow Proclamation. He goes into a locker room and takes off his clothes (his previous incarnation's). Rory and Amy have followed him. While Rory thinks it only fair to look away as the Doctor undresses, Amy continues to watch him avidly. The Doctor puts on fresh clothes and then goes up to the roof, followed by Amy and Rory. He confronts the giant eyeball that is the Atraxi and tells them how important Earth is. He shows them a montage of creatures he has defeated as well as images of his ten previous selves. Thus warned, the Atraxi depart for good.
The TARDIS key begins to glow and the Doctor realises that it has completed its repairs. He races back to Amy's garden and enters the newly refurbished console room. Amy reaches her garden as the TARDIS dematerialises.
When the Doctor returns for Amy at night he discovers that a further two years have elapsed and she is not very happy about it. He asks her if she would like to be his travelling companion. She refuses but when she sees inside the TARDIS she changes her mind. She says that she will go with him as long as he promises to have her back in Leadworth by the following morning. When he asks why she gives a vague reply. She asks why her, but he says it is just for companionship. Beside him a scanner displays a line that looks like the crack in her bedroom. As the TARDIS vanishes a shot of her bedroom reveals the cartoons and models that Amy made of herself and the Doctor. A wedding dress can be seen on the back of her door.