A woman named Darla manages to contact the Doctor and summons him to the Dalek homeworld, Skaro. He's impressed and suspicious that she was able to contact him, and Darla explains that her daughter Hannah is at a Dalek prison camp and she needs the Doctor to help her escape. The Doctor notes that no one can escape a Dalek prison camp and takes her hand, realizing that it's cold. He says that it's a trap for him even though Darla doesn't know it, as a Dalek eyestalk emerges from Darla's forehead. A Dalek gunstick protrudes from her palm and she uses it to stun him. A Dalek saucer arrives outside and the Daleks are satisfied that they have acquired the Doctor.
On 21st century Earth, Amy is doing a fashion shoot when her assistant Cassandra informs her that Rory is there. When Amy says that she doesn't have an assistant, Cassandra reminds her that she still does. Amy goes to see Rory in her dressing room and he tells her that she has to sign the divorce papers to make it official. She does and Rory goes outside. The lights on the dressing mirror flicker as Cassandra starts to prepare Amy for the shoot. However, a Dalek eyestalk protrudes from her forehead as she advances on Amy.
Outside, Rory catches the bus. The bus driver looks stoically at him and there's a flash of light.
Rory wakes up later and finds himself in a white room with Amy. The viewport shows a Dalek fleet assembled outside, and Daleks escort the Doctor in. He warns that they're in serious trouble as the floor rises up, depositing them in a vast chamber filled with thousands of Daleks. The TARDIS is standing to one side. The Doctor tells his companions that they're facing the Parliament of Daleks and steps forward, daring them to kill him. However, the Daleks instead order him to save them.
A woman, Oswin, is in her quarters in an underground complex. She barricades the door so that the Daleks can't get inside and then turns on a performance of Carmen to lock out the noise.
Darla enters the room and tells the Doctor that the Prime Minister will speak to them. When he wonders if she still remembers who she was before the Daleks converted her, Darla admits that she can only access the memories of her former life when it is required to complete a mission. The Dalek Prime Minister, a caseless Dalek, addresses the Doctor and asks if he knows of the Dalek Asylum. The Doctor has heard of it as a legendary world where the Daleks send their insane and battle-scarred Daleks to when they can't control them.
A viewing port in the floor opens, revealing the Dalek asylum planet. Darla explains that there are millions of Daleks upon the automated planet. She then plays a signal from the planet, the music from Carmen, but the Daleks don't know what music is. The Doctor tracks the signal back to its source and makes contact with Oswin. She explains that she was the entertainment manager aboard the starliner Alaska until it crashed on the planet a year ago. The Doctor wonders how she's been holding off the Daleks and Oswin admits that she doesn't know. She also talks about how she makes souffles, and the Doctor wonders where she gets the milk.
The Daleks interrupt, saying the conversation is irrelevant, and cut off the signal. The Doctor wonders why the Daleks don't simply destroy the plane and Darla explains that it is surrounded by an impenetrable force field that can only be switched off from the inside. The Doctor realizes that if a starliner can penetrate the force field that surrounds the planet then the insane Daleks can escape and threaten the universe. He suggests that a small assault team penetrate the force field and turn it off, but then realizes that the Daleks are too scared to go. Darla puts a wristband on him and explains that it will protect him from the nanocloud, puts similar devices on Rory and Amy, and leads them to a gravity beam. The Daleks believe that the Doctor requires companions, which is why they abducted Amy and Rory, and the converted humans shove the trio into the gravity beam and down to the planet.
The gravity beams touch down on the ice planet and a man in a white parka looks on in surprise. The man, Harvey goes to investigate and finds Amy lying in the snow. He introduces himself and she runs off to find the others.
A Dalek eyestalk emerges from the snow, locating the Doctor. He introduces himself and hears Carmen playing through its mike. He realizes that it's Oswin and she explains that she hacked the Dalek technology to access the spy system. The Doctor is surprised, pointing out that Dalek technology is notoriously difficult to hack. Amy and Harvey find the Doctor and Harvey tells them that he saw another beam hit nearby. However, they discover that the beam hit an old shaft and Rory was deposited deep beneath the surface.
At the bottom of the shaft, Rory finds wakes up in a chamber filled with dozens of Dalek casings. None of them respond when he looks around.
Harvey takes Amy and the Doctor to one of twelve buried escape pods and explains that he and the crew of the Alaska crashed on the planet two days ago. The Doctor and Amy realize that something is amiss since Oswin said the ship crashed a year ago. Their also surprised when they discover that all of the crew in the pod are long-dead corpses. Harvey insists that he just talked to them, but then a Dalek eyestalk emerges from his forehead and he admits that his body is in better condition because he died outside of the ship.
The Doctor uses a fire extinguisher to drive Harvey back into a compartment and seal him in. He then tells Amy that the nanocloud contains nanobots which transforms any living or dead matter into Dalek drones, adding them to the security system. The Dalek wristbands prevent the nanobots from infecting and changing them. Amy realizes what the Doctor has overlooked: the dead crew are also susceptible to conversion. The corpses stand up, eyestalks emerging from their foreheads, and advance on the duo. The Doctor and Amy make it to the front companion and bar the door, and Amy admits that she's missed that kind of excitement in her life.
Oswin contacts them over the ship's radio and the Doctor again insists that it's impossible to hack Dalek system. She tells them that the floor contains an escape hatch and the Doctor discovers a shaft beneath it. Someone climbed down through the hatch and sealed it behind them. As the Doctor prepares to descend, he asks Amy what's wrong between her and Rory. She admits that they've separated and tells him that there's nothing he can do to fix it. When the Dalek drones try to break down the door, the Doctor checks on the monitor and discovers that one of them is holding Amy's wristband and that she lost it in the confusion.
As Rory examines the casing, one of them activates, swiveling around to track him. The other Daleks slowly activate, chanting "Exterminate." They open fire and Oswin contacts Rory, telling him to get out through a nearby door. He slides beneath it just in time as Oswin closes the door, sealing in the Daleks behind him.
The Doctor and Amy climb down the shaft and the Doctor explains that the nanobots in Amy's system are rebuilding her, starting with her memories. As they head down a hallway, and he says that they're already at work because it's the fourth time he's had to explain it to her.
Oswin directs Rory through the corridors and into a room that she can seal to keep him safe for the time being.
The Doctor and Amy find the primary chamber and hear the Daleks in the distance. The Doctor seals off the room and talks to Oswin, who directs him to a computer alcove that holds a map showing where Rory is. As they talk, Amy clutches at her forehead in pain and then sees people moving through the chamber. In the alcove, the Doctor checks the map and discovers there are Daleks in the chamber. He goes to get Amy, who says that she can see people. The Doctor tells her to concentrate and Amy realizes that she's looking at the injured Daleks. They hide in the computer alcove but one of the Daleks follows them. Impeded by damage, it is unable to fire. The Dalek conversion-drones are climbing down the shaft, cutting off their only means of escape, so the Doctor dares the Dalek to identify him. When it does, he tells it to follow its standing orders and destroy itself. With its gunstick inoperable, the Dalek goes into self-destruct mode and the Doctor programs it to shoot backward and slam into the other Daleks in the chamber, exploding and destroying them all.
Rory hears the explosion and goes back to the chamber. The Doctor is carrying the stunned Amy, who slaps Rory when she wakes up. Oswin warns that Amy will kill them once she undergoes conversion. The Doctor wonders why Oswin hasn't been converted but she assures him that she's shielded inside of her chamber, and has been sabotaging the automated systems. He still believes that it isn't possible for an entertainment manager to hack Dalek systems and is intrigued about how she can make souffles when she has no milk. Meanwhile, Oswin checks the Dalek databases and discovers numerous references to the Doctor as "The Predator."
The Doctor discovers a teleporter in the chamber and devises a plan, and asks Oswin how quickly she can drop the force field. She says that she can bring it down in a few seconds, and the Doctor says that he can boost the teleporter power to beam them back to the Dalek ship, before the ship blows up the planet when the force field goes down. He asks Oswin to drop the force field and come to the so she can escape as well, but she doesn't believe they'll wait for her. She gives him a map showing him where he can find her and the Doctor prepares to leave. Before he goes, he tells Rory to take Amy and escape if he doesn't come back in time, and then tells Amy to remember that she has to fight the conversion process and remember love.
As the Doctor heads for Oswin's chamber, Amy and Rory wait. He tries to give her his wristband, explaining that it will take longer to convert him and that she'll be protected from further alteration. When Amy wonders why it will take longer, he reluctantly explains that he loves her more because she was the one who kicked him out, and that he waited two thousand years for her. A furious Amy slaps him and explains that she gave him up because she knew he wanted children and that she couldn't have them after Demon's Run. Crying, she tells Rory not to give her his wristband... and they realize that the Doctor has already placed his wristband on her.
As the Doctor approaches Oswin's chamber, she warns him that the Intensive Care unit is ahead. The "patients" inside are Daleks who survived wars on particular planets, and the Doctor recognizes the names as planets where he fought the Daleks. The Daleks activate and move in on him, and the Doctor discovers that the door to Oswin's chamber is sealed. As she tries to find the release code, the Daleks close in... and then drop back, harmless. When the Doctor wonders what Oswin did, she explains that she hacked the Dalek telepathic net and erased their memories of the Doctors. Shocked, the Doctor says that even he hasn't been able to do that.
When the door opens, the Doctor enters the next chamber and then hesitates, shocked. He asks Oswin if the chamber looks real to her, and then tells her that she is imagining it because the reality is too terrible to face. He then looks at the Dalek in the chamber, chained in place. It speaks in a Dalek voice, saying that it is Oswin. The Doctor realizes that she was the one who escaped the pod and climbed down to the asylum... only to undergo full conversion.
The Oswin-Dalek breaks its chains and advances on the Doctor, chanting "Exterminate," while Oswin looks helplessly on within her chamber. However, it hesitates at the last moment and Oswin asks the Doctor why the Daleks hate him so much. She knows that the Daleks have become stronger due to their fear of him, and the Doctor admits that he knew it as well but couldn't stop fighting them. Oswin drops the force field and warns the Doctor that the Daleks in orbit have begun their assault. Fighting the Dalek programming, Oswin tells the Doctor that she fought the Daleks and is a human being, and asks the Doctor to remember her.
The Doctor runs back to the teleport chamber while Amy and Rory wait... and vow to wait no matter what. They kiss just as the Doctor arrives, and he has to activate the teleporter while they're distracted.
The Daleks on the Parliament ship detect an incoming teleport beam and prepare for attack. The Doctor emerges from the TARDIS and explains that he aimed the teleport beam to place him inside the TARDIS. Darla and the Daleks have no idea who he is, however, and the Doctor realizes that Oswin's erasure of his datafiles extended to all of the Daleks, not just the ones in the asylum. He bids them goodbye and leaves in the TARDIS as the baffled Daleks wonder who "the Doctor" is.
The Doctor takes the TARDIS to Earth and drops off Amy and Rory. They go into their flat together. He then dances inside the TARDIS, realizing that his greatest enemies no longer know who he is.