A very pretty girl in a red dress listens to 'Carmen' while hammering planks across a doorway. She pulls a burnt soufflé from the oven, and then dictates a log entry that says it is day 363 and the terror continues. Daleks bang on her door demanding to be let in. She turns up the music.
The Doctor paces round angrily until a Dalek announces that they have arrived and the Prime Minister will speak with him. As he approaches, he passes the woman whom tricked him. He asks if she remembers who she was and that she has a daughter. She says she remembers when she needs to for deep cover and that she knows about the daughter because she has read her file. She seems amused by this. The Doctor approaches the Prime Minister, a Dalek creature encased in glass.
The Prime Minister asks if the Doctor has heard of the Dalek Asylum. He replies that he has heard of a place where the Daleks send their insane and battle scarred. He wonders why they don't just kill them. The Dalek replies that the Daleks consider the hatred felt by the insane to be beautiful and it would be offensive to destroy it. He wonders if this is why they have never been able to kill the Doctor.
A hole opens in the floor allowing Amy and Rory to look down onto a planet below. This is the Asylum of the Daleks where uncounted Daleks have been sent. The Asylum is automated and therefore unsupervised. The Daleks play 'Carmen', saying that it is a transmission being received from the Asylum. The Doctor says that he played triangle before asking if anyone has tried to contact the broadcaster. The Prime Minister and Darla exchange a glance. The Doctor makes a call down. The young woman in red runs across to her radio and asks who is talking and if they are real. She identifies herself as Oswin Oswald, junior entertainments manager on the Starship Alaska. She says that the ship has crashed and she is shipwrecked but she isn't sure of her location and the rest of the crew is missing. She has provisions but is under regular attack by Daleks.
The Doctor asks her what she has been doing for a year and she replies that she has been making soufflés. The Doctor asks where she gets the milk, at which point the Dalek Supreme says the conversation is irrelevant. The Doctor says that it isn't: if someone can get into the asylum the Daleks can get out. The Supreme says that the asylum must be cleansed. There is a force field round the planet but it can only be turned off from inside. The Doctor asks why they don't do it themselves. He is met by silence and realises that they are too scared to go themselves. The Supreme says that the Predator of the Daleks will be deployed. The Doctor says that the Daleks have no Predator until Darla explains that Predator is the name they use for the Doctor.
The Doctor has a device strapped to his wrist to protect him from 'the nano-cloud'. He is told a gravity beam will land him close to the source of the transmission. Rory and Amy are given similar devices because, as the Supreme says, it is known that the Doctor needs companions. The Doctor tells Amy not to be scared but she says, "Who's scared? Geronimo!" The three of them are fired down a gravity beam to the planet's surface.
Amy lands in the snow near a man who is drilling at a hatch in the ground. She shouts for Rory. The man says he is Harvey and asks if they are the rescue mission.
The Doctor is also in the snow. Dalek eye-stalks protrude from the snow and observe him. When he notices them, the music from 'Carmen' starts. It is replaced by Oswin's voice. The Doctor asks her how she is using Dalek technology. She tells him it easy to hack tough he disagrees with this. She tells him she is somewhere underground. The signal begins to break up when Amy and Harvey arrive. Harvey tells them that another beam came down over the hill. When they get there they see a deep shaft into the planet's interior.
At the bottom the shaft lies Rory. He recovers slowly to find himself surrounded by Daleks. They are silent and immobile. He pushes one but there is no response. He begins to relax.
Harvey takes the Doctor and Amy to an escape pod, saying that the ship (the Alaska) crashed two days earlier. This is a puzzle since Oswin says she has been there a year. The rest of the crew members in the pod are long dead and almost skeletons. Harvey is shocked because he was only talking to them two hours and then he remembers that he died out in the snow. He develops a Dalek eye-stalk. The Doctor and Amy push him through a hatch. The Doctor says that the nano-cloud transforms anything non-Dalek so that they become a part of the defence rather than a threat. He adds that this works on anything organic, living or dead. At this, the corpses develop eye-stalks and lumber into life. The Doctor and Amy struggle through them and through another hatch. Amy says how much she has missed this sort of adventure.
Oswin calls them, making fun of the Doctor's chin. The doctor asks how she can keep hacking into Dalek technology. She asks if there is a word that means 'total screaming genius and a bit sexy'. He tells her there is: 'Doctor'. She tells them that there is a way out through a hatch in the floor. While the Doctor is opening the hatch he asks what happened between Amy and Rory. She says that they just split up and there is nothing he can do to fix it. Beneath the hatch is a long shaft with a rope ladder leading down. Just then, the Doctor notices the corpses on a viewscreen showing him Amy's wrist protector. She asks what will happen to her without it.
Rory examines one of the Daleks, moving its eye section. He is perturbed when it swings back into its original position. As he steps back he bumps a metal rod. The sound causes a number of Daleks to wake up. The one in front of him says, "Eh-eh-eh-eh-eh-eggs." Looking at the floor, Rory sees one of the spheres is missing from the Dalek's body and picks it up. He asks if this is the egg. The Dalek replies, "Eggs-term-in-ate. Exterminate." The other Daleks take up this refrain. As they start to shoot, Rory rolls past them looking for a way out. Oswin's voice tells him to run to the door at the end. As he approaches it opens and then closes as he slides through, locking the Daleks out.
Oswin introduces herself and asks his name. When he tells her she says the first boy she fancied was called Rory before changing her mind and saying it was a girl called Nina. She adds that she is just flirting to keep him cheerful.
As Amy descends the ladder she asks what is happening to her. The Doctor tells her she is being rewritten by nano-genes. The physical changes will come later but her mind is already being affected. When she asks how he knows this he tells her that this is the fourth time they have had this conversation. She says she is scared and he tells her to hang onto this: scared isn't Dalek.
Oswin guides Rory to a safe place and then contacts the Doctor. She tells him she is ending him a map to get him to Rory's location. While she does this, Amy steps through another door and finds herself in a chamber where people are laughing and dancing. The Doctor runs after her but she says it is safe, there are only people there. He tells her to look again; the nano-cloud is affecting her perception. This time she realises they are actually Daleks, some of them revolving on the spot. One of the Daleks follows them as they run out and corners them. It tries to exterminate them but its gun won't work. The Doctor tells it to access its files to see who he is. It recognises him as the Predator. He tells it to follow its standing orders. Knowing it must kill him it begins to self destruct. The Doctor uses his screwdriver to send it in reverse and it blows up in the chamber containing the other Daleks, killing them all.
Rory runs into the chamber and surveys the damage. He asks, "Who killed all the Daleks?" the Doctor enters, carrying Amy. He says, "Who do you think?" Rory bends over her and asks if she remembers him. She slaps him. Oswin is worried that she is so angry - this seems to be the start of the conversion. Amy sits up and observes that "Somebody has never been to Scotland."
The Doctor is full of questions. Why hasn't Oswin been converted? How can a junior entertainments officer hack the systems of the most advanced warrior race the universe has ever seen? More than that, he wonders where she gets the milk for her soufflés. He then says that his plan is to defeat the Daleks, rescue Oswin and repair Amy and Rory's marriage. Amy says that she can count three lost causes. The Doctor tells Oswin that as soon as the force-field is turned off the Daleks in the ship above will burn the planet with them on it. He asks if Oswin can turn off the force field. She asks why she would do that. He tells her that he can boost the internal teleport to take them back to the Dalek ship. Oswin tells him that she will only drop the force-field once he has come to rescue her.
After the Doctor has rigged the teleport he tells Rory to go without him if he has to. He tells Amy that the nano-genes are extracting love from her and her best defence is to not let them. After the Doctor has gone, Rory tries to give his wristband to Amy, saying that he has more love than her. He says he has always loved her more than she has loved him. She slaps him and says that she didn't kick him out but she let him go because he wants children and since Demons Run she hasn't been able to have children. Rory still tries to give her his wristband only to find that she is wearing the Doctor's. She says that he is a Time Lord and probably doesn't need it.
When the Doctor arrives at Oswin's door he finds the most damaged Daleks, mentally. She tells him that they are the survivors of particular wars; Spiridon, Kembel, Aridius, Vulcan, Exxilon. The Doctor notes that these were all Daleks who survived him. They come to life, intoning "Doc-tor." Oswin thinks this is weird, these Daleks never wake up. The Daleks close in on the Doctor, trapping him against a door. As he screams for help, Oswin hacks the Daleks' telepathic web and makes them forget the Doctor. They withdraw in silence. Oswin opens the final door.
She tells him to come in and rescue her and show her the stars. The Doctor is aghast. He is not looking at a girl but a Dalek. He tells her she is living a dream because the truth is too terrible. After she escaped down the rope ladder she was transformed into a Dalek but because she was a genius they did a full conversion. Oswin finally recognises the truth. He says that the clue was the milk and the eggs to make the soufflés. She hears the word 'eggs' and starts to say "Eggs-term-in ate!" Just as the Doctor fears for his life she begins to sob. She asks him why the Daleks hate him so much. They have grown stronger because they fear him. He says he knows and he tried to stop. She tells him to run because she has turned off the planet's force-field. As he turns to go she declares, "I am Oswin Oswald. I fought the Daleks and I am human. Remember me."
Explosions begin and Rory asks how long they can wait. Amy tells him they will wait the rest of their lives and they kiss. The Doctor arrives and tells them they are good top go. Neither of them responds so he presses the button. As the Dalek missiles hit and the planet explodes they teleport away.
On the ship, the Daleks report the Asylum is destroyed but they are under attack via teleport. The Doctor steps out of the TARDIS saying he is so good he can teleport with pinpoint accuracy. The Daleks ask who he is. He tells them he is the Doctor, the Oncoming Storm, and the Predator. Darla says that titles are meaningless and asks who he really is. This is when the Doctor realises he has been wiped from the minds of all of the Daleks. As he steps back into the TARDIS the Daleks begin a chorus of "Doctor who? Doctor who?"
He drops Amy and Rory off at home where they enter their house together. The Doctor dances around his TARDIS console, chanting "Doctor who! Doctor who!"