The TARDIS materializes in an underground bunker and Rose and the Doctor emerge. The Doctor notes they're in Utah in 2012 and have been drawn off course by a signal. The lights come on and they find themselves in a museum containing alien artifacts. The Doctor concludes someone was calling for help. When he touches a case, an alarm goes off and security guards charge in to hold them at gunpoint.
Billionaire Henry van Statten arrives amidst a flurry of activity and meets with his new aide Goddard and his English expert in aliens, Adam Mitchell. They check in on their newest acquisition and then van Statten confronts the Doctor and wants to know what he was doing near his one living specimen in The Cage. The Doctor taunts van Statten into showing him his new acquisition, his "metaltron," while Rose is handed off to Adam.
The Doctor enters the darkened Cage and offers his help, but then the Metaltron lights up revealing it's a…Dalek. The Doctor tries to get out but van Statten leaves him in there to see what happens. But it soon becomes clear the Dalek is restrained and its weapon harmless. The Doctor recovers from his panic and taunts the Dalek when it asks for orders. He reveals the Dalek race was wiped out and the Dalek asks if the Doctor destroyed them. The Doctor reluctantly admits he did, having no choice, and that the Time Lords are dead as well. The Dalek points out they are the same, being the only ones of their respective species. The Doctor acknowledges it is right, then grabs a lever and feeds electricity into it to kill it.
Van Statten orders his guards to stop the Doctor and demands that the Dalek talk to him, but it refuses. Meanwhile, Rose tours Adam's laboratory and suggests he might want to get out of his lab and see what's out there, but he's skeptical. Adam reveals he's tapped into the communication system and shows Rose the Dalek. Van Statten's head scientist Simmons is torturing the Dalek to get it to talk.
The Doctor briefs van Statten on the Dalek's origins and Goddard reveals it fell out of the sky. The Doctor determines it fell through time and van Statten realizes he has yet another alien for his collection. He runs the Doctor through a bio-scan and discovers his two hearts, which he plans to patent. The Doctor realizes that van Statten has been using alien technology to get new patents and make his fortune. The Doctor tries to warn van Statten who ignores him.
Rose is upset when she sees the Dalek being tortured and demands she be taken to it. Adam takes her in and Rose introduces herself to the Dalek, asking its name. It says it's in pain and asks if she fears it. She says no and touches it in sympathy. When she does it extrapolates from her genetic material and initiates reconstruction, breaking free. Simmons approaches it and it crushes his skull with its sucker-arm attachment. The Doctor suggests van Statten free him if he wants them to live.
The Dalek overrides the Cage door lock as the Doctor and the others look on. It emerges and the guards open fire while Rose and Adam run. The Dalek ignores them and destroys the video monitor, drawing on the base electricity to further regenerate itself. It then absorbs the power from the nearest seven states and all the information of the Internet, then opens fire with its repowered weapon. More guards arrive while Rose and Adam run with their assigned guard, De Maggio. The guards open fire but the bullets melt against its force field. It then fires on the guards, killing them. Van Statten insists that the guards stop firing but his orders soon become moot when the Dalek kills them all.
Goddard shows the Doctor a layout of the facility and he suggests they distribute the alien weapons to the remaining staff. Rose and the others run up the stairs but the Dalek levitates and follows. De Maggio sends them off and tries to delay it at the cost of her own life. Van Statten can't understand why the Dalek won't negotiate and only wants to kill.
More guards and staff focus fire on the Dalek on the Doctor's orders while Rose and Adam get clear. The Dalek is unaffected by the fire but seems interested in Rose. The Doctor realizes the Dalek wants them to witness its invulnerability. It then levitates and sets off the sprinklers and sends an electrical blast through the water, electrocuting everyone present. Van Statten suggests they evacuate but they're cut off due to the lack of power. The Doctor suggests they use emergency power to seal the bulkheads and van Statten volunteers his genius.
The Dalek demands to speak to the Doctor and reveals that by absorbing the DNA of a time traveller it was able to reconstitute itself. It acknowledges that there are no Daleks on Earth and announces it will destroy and conquer sans any new orders. When it asks what to do, the Doctor suggests that it kill itself. The Dalek declares the Doctor would make a good Dalek himself, then cuts off communication.
Rose and Adam head for the exit as van Statten works to seal off the lower levels before the Dalek can emerge. Van Statten gets temporary power to the bulkheads and the Doctor has no choice but to seal them…with Rose trapped on the other side as Adam just barely makes it through. Rose calls the Doctor on her cellphone as the Dalek approaches her and assures him that it wasn't his fault. As the Doctor listens in, the Dalek shrieks "Exterminate!" and opens fire.
The Doctor is grief-stricken and unimpressed by van Statten's apology. The Doctor blames him for all of the deaths and points out his self-serving nature. However, Rose isn't dead – the Dalek hesitated due to the infusion of Rose's DNA. It realizes it has been contaminated with human emotions. The Dalek contacts the Doctor again and threatens to kill Rose if the Doctor doesn't open the bulkhead. The Doctor refuses to let Rose die again and opens the vault. Adam reveals there are weapons in his lab and the Doctor goes there to find a hand cannon.
While they wait for the elevator, Rose talks to the Dalek, which is puzzled by its inability to kill her and the emotions consuming it. They emerge in van Statten's office and it prepares to kill him, but Rose intervenes and it says the one thing it wants is freedom. The Dalek leaves and then blasts a hole in the ceiling to feel the sunlight. Then it opens its casing so it can feel the sunlight.
The Doctor arrives and demands to kill it but Rose refuses, pointing out it couldn't kill her or van Statten . The Doctor drops his gun and the Dalek wonders what the point is of either one of them surviving. The Doctor points out that Rose's DNA is mutating it so it's no longer "pure." The Dalek asks Rose to give it a final order, to die. Rose reluctantly agrees and admits she is frightened – the Dalek admits it as well. Rose gets clear as the Dalek closes the casing, levitates into the air, then self-destructs.
Goddard takes command and orders the guards to wipe van Statten's memory as penalty for his responsibility in the deaths. The Doctor reveals he's the only one of his kind left and would know it if there were any other Time Lords. Adam shows up to tell them Goddard is closing down the base and Rose suggests they take Adam with them. The Doctor reluctantly agrees and they all go into the TARDIS and leave.