The TARDIS materializes in a dark room and the Doctor informs Rose that a signal has drawn the TARDIS there, in the year 2012. They are deep beneath the Utah desert. The Doctor turns on the lights to reveal dozens of cases of alien artifacts and specimens. None of them account for the signal, which is asking for help. Security guards abruptly pour into the vault and take the Doctor and Rose prisoner.
Henry van Statten, the owner of the entire facility, arrives by helicopter and immediately fires his assistant, has his memory wiped, and thrown out on the road. He brings in his next assistant, Diana Goddard, and the “English kid,” Adam Mitchell, who handles buying the alien artifacts. van Statten wants to know the status of his “pet” and Goddard calls down to Simmons. He says that it’s screaming.
The Doctor and Rose are brought before van Statten and the Doctor demonstrates his knowledge of artifacts by activating a newly purchased item. The Doctor admits he has no idea who van Statten is and admits he stumbled in by mistake. van Statten notes that the Doctor was captured near The Cage, where he keeps his one living specimen. The Doctor taunts the millionaire into showing him his specimen while Rose is sent to accompany Adam.
van Statten explains that the creature is inside of a shell, and has shielded itself from scans. He calls it a “metaltron” and invites the Doctor inside to examine it. The Doctor enters the chamber and van Statten orders Simmons to close the door and keep it closed until they get a result. The creature within says a single word, “Dok-tor,” and recognizes him. The lights come up and a Dalek is revealed, chained to the walls.
The Doctor panics and demands to be let out, but soon realizes the Dalek’s gunstick is powerless and it’s immobilized. The Doctor taunts it, noting that if it can’t kill than it’s no longer a Dalek. It insists it’s a soldier bred to receive orders, and it demands orders. The Doctor informs it that it’s race is dead and says that he made it happen. he draws back, upset, and admits that the Time Lords were wiped out as well and everyone was killed in the last great Time War. The Dalek calls him a coward but the Doctor informs it that no one is coming. The Doctor pulls down a lever, electrocuting the creature. van Statten tells his security team to get the Doctor out. van Statten demands that it respond to him but it ignores him. He tells Simmons to make it talk again, no matter what it takes.
Adam shows Rose his laboratory and boasts of how aliens exist. Rose is amused and wonders if he wants to get out there to see everything. Adam says he’d do anything to see the universe. He explains that van Statten’s agents recruited him after he hacked the U.S. computer defense system. He shows Rose that he’s hacked into the communication system and they watch as Simmons tortures the Dalek.
The Doctor tells van Statten how the Dalek race were genetically engineered. Goddard explains that it fell to earth and the Doctor concludes it fell through time. van Statten realizes the Doctor is also a unique alien. He’s stripped to the waist and taken to a laboratory for analysis. van Statten is intrigued to realize the Doctor has two hearts and the Doctor realizes the millionaire has developed technology from alien artifacts. The Doctor tries to warn van Statten that no one is safe but the millionaire ignores him.
Adam takes Rose to see the Dalek. She introduces herself and asks if it’s in pain. It says that it is and asks if she fears it. She says she doesn’t and the Dalek says it will die alone. Rose touches it in a gesture of comfort, and the Dalek’s armor glows with her handprint. It announces that it’s extrapolated the genetic material of a time traveler and regenerates itself, breaking its chains. Simmons runs in and the Dalek kills him with its sucker. Rose and Adam run out into the Cage’s antechamber and the alert is sounded.
The Doctor tells van Statten to free him if he wants to live. The millionaire does so and they go downstairs. Rose, Adam, and two guards are in the antechamber as the Cage is sealed. The Doctor warns that the Dalek can easily open the combination. It does so and the guards open fire. The Dalek ignores them and taps into the monitor, draining the base’s electricity to further regenerate itself. It also absorbs the Internet, gaining vast knowledge. One of the guards, De Maggio, gets Rose and Adam out.
The Dalek makes its way out, easily killing the guards while its force field makes it immune to their bullets. van Statten tells his men to stop firing for fear of damaging his creation. It’s too late, however: it’s killed all of the guards. Goddard points out where the alien weaponry is but warns the Dalek is between them and the weapons. The Doctor tells van Statten to give weapons to everyone.
Rose, Adam, and De Maggio come to a flight of stairs and run up them, confident the Dalek can’t follow. It rises into the air on an anti-gravity field and moves toward them. De Maggio tells Adam to get Rose out while she tries to delay it. The Dalek easily disposes of her.
The Doctor tries to explain to van Statten that the Dalek will kill and keep killing until every human on the planet is dead.
The guards and security staff move into position and the Doctor advises them to mass their fire on the eye stalk. Rose and Adam run past and then wait as the Dalek arrives. It spots Rose, who notices that it focused specifically on her. The Dalek moves into the center of the chamber and everyone opens fire. It lifts into the air and fires at the sprinkler system, activating it. The Dalek then fires an electrical blast into the puddles of water, electrocuting all of the attackers. The Doctor, watching on the monitor, realizes that it wanted them to see how powerful it is. van Statten suggests abandoning the facility but Goddard points out the elevators have no power. The Doctor suggests rerouting the emergency generators and van Statten insists he can do it.
The Dalek contacts the Doctor via the monitor screen and explains how it regenerated itself. It has determined there are no Daleks and has no orders, so it plans to follow the Dalek instinct and destroy and conquer. The Doctor wonders what the point is and then gives it an order: to kill itself. The Dalek observes that the Doctor would make a good Dalek.
van Statten taps into the emergency power reserves while Rose calls the Doctor on her cell phone. He tells her to keep moving and get out before he seals off the vault. The Dalek proceeds up the stairs behind Rose and Adam. van Statten can’t maintain power and the Doctor has no choice but to seal the bulkheads. He says “Sorry” to Rose and throws the switch. Adam gets through but Rose is sealed in. She says she wouldn’t have missed their travels for the world. The Dalek moves in and the Doctor hears it cry “Exterminate!” The Doctor blames van Statten and wonders if it was worth all the deaths.
Rose looks up: she’s still alive. She wonders why the Dalek hasn’t killed her and the Dalek explains that it fears her fear. It fires wildly and wonders what else Rose has given her besides life.
Adam meets with the others as the Dalek opens up the communication channel and tells them to free it or it will kill Rose. The Doctor refuses to let her die and opens the vault door. They consider their options and Adam says he has some uncatalogued weapons. The Doctor finds a working one and goes to fight the Dalek.
As the Dalek ascends in the elevator, it asks Rose what it is any more. They arrive at the top level and Rose tells van Statten not to move. The Dalek demand answers from van Statten, wondering why it tortured him. He tries to defend himself but it is unimpressed and prepares to kill home. Rose intervenes and says it doesn’t have to kill and asks what it wants. It says it wants freedom.
The Dalek takes Rose to the central hangar and the Dalek blasts a hole in the ceiling to reveal the sunlight. The Dalek wonders what it feels like and then opens its casing, revealing the organic component inside. It basks in the sunlight for a moment.
The Doctor arrives and threatens to kill it, but Rose says the Dalek is changing and wondering what he’s changing into. The Doctor breaks down and admits his people are dead, and the Dalek wonders what the point is in surviving. The Doctor tells it that it’s mutating into something new and apologizes. When Rose wonders why, he explains that Daleks can’t change. The Dalek begs Rose to give it the order to kill itself, because it can’t live with itself in this state. Rose takes pity on it and gives the order. It asks if she’s frightened and admits that it is as well. With one final “Exterminate,” it activates its self-destruct mechanism and is disintegrated.
Goddard orders the remaining guards to wipe van Statten’s memory and take him away.
The Doctor and Rose return to the TARDIS and the Doctor admits he’s the last Time Lord. He’s confident that there’s no one else of his race. Adam arrives to tell them Goddard is closing the base and they have to leave. Rose notes that Adam wanted to see the stars. The Doctor isn’t sympathetic given Adam abandoned Rose but agrees to take Adam along with them. After a moment, Adam enters the TARDIS just before it dematerializes.