Henry van Statten arrives at the bunker to view his collection for his birthday. In passing, he also orders that the US President be replaced; when his personal assistant, Polkowski, politely questions this order, van Statten fires him on the spot, and his guards drag Polkowski away to erase his memory and dump him on the side of the road somewhere. Van Statten’s new PA, Diana Goddard, reports that intruders have been captured in the vault, and van Statten orders that they be brought to him for questioning. Afterwards, he intends to visit his “pet,” and Goddard thus contacts Simmons, who is in charge of torturing the alien captive. He’s been unable to get it to speak, but he’s certainly got it screaming...

The Doctor and Rose are brought before van Statten, who is examining the new alien artefacts bought at auction by another of his employees, a young Englishman named Adam. The Doctor shows van Statten how to use one of the artefacts, a musical instrument, but van Statten then tosses it aside and demands to know how the Doctor managed to get into his vault, right next to the cage containing van Statten’s one living specimen. The Doctor is unimpressed by the rich man’s arrogance, but van Statten, confident that he’s in charge here, orders Adam to keep an eye on Rose while he takes the Doctor to the cage to see what will happen. Van Statten and the Doctor descend to the cage, a sealed vault within the vault, and Simmons offers the Doctor a pair of rubber gloves, claiming that the last person to touch the “Metaltron” burst into flames. The Doctor steps into the cage, and van Statten seals the door behind him, ordering the guards -- Bywater and Di Maggio -- not to open it until they get a result.

Inside the darkened vault, the Doctor sees the abandoned instruments of torture, and he approaches the alien, introducing himself and offering his help. But to his horror, the lights go on to reveal that he’s facing a Dalek, chained up and immobile. The Dalek tries to exterminate its enemy, but after a moment of blind panic, the Doctor realises that its gun isn’t working. Simultaneously relieved and enraged, the Doctor viciously lashes out at the powerless Dalek, revealing that it’s the last of its kind; he, the Doctor, destroyed all other Daleks in existence. He then falls silent, as if he’s only just realising what he’s done. When the Dalek questions him about the Time Lords, the Doctor is forced to admit that they too are dead, victims of the Time War; he and the Dalek are the last of their kinds in the Universe. When the Dalek points out that this gives them something in common, the infuriated Doctor boosts power through the Dalek’s restraints, electrocuting it. Van Statten sends guards in to cut the power, and as they drag the Doctor out, he demands that they destroy the Dalek before it’s too late. Van Statten ignores him and addresses the Dalek, pointing out that he’s saved its life and demanding that it speak to him. It does not, and he thus puts Simmons back to work.

Adam shows Rose his workshop, a cluttered room full of unclassified alien artefacts. Adam was a child prodigy who nearly started a world war by hacking the US defence system when he was eight years old; van Statten’s agents found him and put him to work here, identifying and cataloguing the artefacts in van Statten’s collection. Adam tells Rose that his dream is to get out and see the Universe for himself, though he doesn’t believe this will happen in his lifetime. Something about his boyish enthusiasm reminds Rose of the Doctor. She asks Adam about the alien in the cage, and he admits that, although van Statten likes to keep it private, Adam has hacked into the base’s communications system so he can see it for himself. He does so now, partly to impress Rose, but he and Rose see that Simmons is torturing the creature, and the appalled Rose demands that Adam take her down there at once.

The Doctor tries to convince van Statten that the Dalek poses a terrible threat; it is the only survivor of the time war between the Daleks and the Doctor’s own people, and, like all Daleks, it has been genetically engineered to have no emotions but hatred. According to Goddard, it has been dormant for 50 years, passing from collector to collector after crashing to Earth in the Ascension Islands, and as far as van Statten is concerned, there’s no reason to believe it will ever escape from its cage. In any case, he’s now more interested in learning about his new alien captive. The Doctor is stripped down and placed in a device that scans his body, putting him through some pain as it determines that he has two hearts. The Doctor realises that van Statten has made his money by scavenging alien technology and patenting the reverse-engineered results. Despite his disgust for van Statten, the Doctor makes another heartfelt attempt to convince him that the Dalek must be destroyed; now that it knows the Doctor is here, it has a reason to break free, and if it does, nobody on the planet will be safe. van Statten ignores him, and continues the scan.

Adam uses his emergency pass to get Rose into the cage, but warns her not to get too close to the Dalek. Knowing only that it’s been tortured, Rose tells it that her friend, the Doctor, can help it. The Dalek, reacting to the Doctor’s name, tells Rose that it is in terrible pain, and claims to welcome death now that it’s met one human who does not secretly fear it. Before Adam can stop her, Rose rests her hand on the Dalek’s casing out of pity... and the Dalek absorbs DNA from her handprint, extrapolates her genetic material, and begins a cellular regeneration process, healing itself. Rose backs away as the Dalek pulls itself free, snapping the chains that held it down. Simmons storms into the cage, and scoffs when the Dalek raises its sucker arm towards him... until the sucker snaps forward, clamps onto his face, and crushes his skull.

Rose and Adam flee from the cage, and Bywater seals the door behind them and announces a red alert. Upstairs, van Statten and the Doctor hear the alarms blaring, and the Doctor orders the stunned van Statten to free him if he wants to live. They return to van Statten’s office, where Bywater contacts them and assures them that the cage has been secured. However, it takes the Dalek mere seconds to break the code and open the door. Bywater orders Di Maggio to get Rose and Adam to safety while he holds off the Dalek; however, bullets have little effect on it, and it trundles over to the computer and smashes its sucker arm through the screen, drawing energy and data directly into its body. As the Dalek’s armour repairs itself, power goes down throughout the complex; soon the base is down to emergency power, the west coast of America is experiencing a blackout, and the Dalek has absorbed knowledge from the entire Internet, learning everything it needs to about the planet Earth. Its gun-stick is fully powered up, and the last of the Daleks is ready to take action.

Di Maggio leads Rose and Adam away as guards rush forward to surround the cage. Bywater rushes down the corridor to join them, but the Dalek emerges from the cage and guns him down before he can reach safety. The guards open fire on the Dalek, but van Statten orders them to stop, insisting that the prize of his collection must not be harmed. In any case, the Dalek is generating a force field that melts the bullets before they so much as scratch its armour, and it swivels about in place, its top and torso moving independently from its base, until it has slaughtered every single guard in the corridor. As it begins moving forward, van Statten suggests sealing the vault, but the Doctor refuses to do so while Rose is trapped inside. The Dalek is now between them and the alien weapons in the collection, but it’s heading for the weapons testing facility; the Doctor thus advises Goddard to distribute weapons to everyone in the facility. Van Statten wants to try negotiating, but the Doctor flatly informs him that the Dalek’s only desire is to kill everything that isn’t a Dalek.

Rose, Adam and Di Maggio reach the stairwell and climb a flight of steps. The Dalek seems stymied by the stairs, and Di Maggio offers it the chance to surrender and discuss terms. But instead, it reveals that it has the ability to hover. As it begins to float up the stairs, Di Maggio sends Adam and Rose to safety while she stays behind to delay the Dalek; as they flee, they hear it exterminate her. Rose and Adam rush through a vast storage chamber in the weapons testing facility, where guards, technicians and scientists are gathering to hold back the Dalek; however, as the Dalek enters the chamber behind them, it seems to focus in on Rose. Adam dismisses Rose’s uneasy feeling, but she’s convinced that the Dalek was looking directly at her, as if acknowledging her existence in some way...

The Doctor orders the guard commander to concentrate his fire on the Dalek’s eyepiece, but sadly the commander is over-confident. When the cameras go on in van Statten’s office, the Doctor realises that the Dalek wants them to see what’s going to happen. As the guards open fire on the Dalek, it rises up into the air and shoots the fire alarm, triggering the chamber’s sprinkler systems -- and once the bay is soaked, the Dalek opens fire. The water on the floor conducts the charge of the blast, and the Dalek need only fire twice to exterminate every single human in the room. The Dalek then addresses the Doctor, explaining that it was able to regenerate itself by extrapolating the DNA of a time-traveller. However, it has now confirmed that there is no sign of Dalek life anywhere in range, and without orders, it is at a loss. The Doctor thus orders it to kill itself and erase the Dalek scourge from the Universe; however, the Dalek is committed to the survival of its species, even if it is the only one of its kind. It signs off as the Doctor raves furiously at it, telling him that he would make a good Dalek himself.

The Doctor now has no choice but to seal the vault. Van Statten, finally comprehending how much danger he’s in, agrees to help the Doctor to bypass the security codes and re-route emergency power to the bulkheads. The Doctor calls Rose on her cellphone and warns her that he’s about to seal off the vault at level 46, and she and Adam run for it. Van Statten finishes his work, but the power is failing, and the Doctor is forced to lower the bulkheads for fear that he won’t be able to. Adam manages to slide under the bulkhead as it descends, but Rose is trapped on the other side. As the Dalek closes in on her, Rose tearfully tells the Doctor not to blame himself -- and the horrified Doctor hears the Dalek open fire. He turns on van Statten, enraged, pointing out that he could have killed the Dalek back in the cell if van Statten hadn’t stopped him; now Rose is dead, all because van Statten didn’t want anything to break up his precious collection.

But Rose is in fact still alive, and the Dalek is as surprised as she is. It fires to either side of her, but for some reason it can’t bring itself to kill her, for it finds that it comprehends her fear. When it took her DNA, it took much more than just the ability to regenerate itself...

When Adam arrives in van Statten’s office, the Doctor lashes out at him for abandoning Rose, but Adam in turn points out that the Doctor’s the one who sealed her in the vault. Before the argument can get ugly, however, the Dalek contacts them and reveals that Rose is still alive -- but she won’t be for long unless the Doctor opens the vault and lets the Dalek out. Rose tells him not to give in, but he can’t bear to lose her a second time, and he thus opens the bulkhead. They are now defenceless against the approaching Dalek -- at least until Adam reveals that his workshop contains a number of alien weapons that have yet to be catalogued. Aware that van Statten tends to dispose of his staff and wipe their memories, Adam held onto a few choice gadgets in case he ever needed to fight his way out of the bunker. The Doctor sorts through them, and soon finds a weapon capable of destroying even a Dalek.

As the Dalek approaches van Statten’s office, Rose begs it not to kill him, but it doesn’t understand why it shouldn’t; its function is to kill, and it has no idea why it’s allowing Rose to live. The Dalek confronts van Statten and demands to know why he tortured it, and although he claims at first that he was just trying to get through to it, to communicate so he could help it, he finally breaks down and admits that he just wanted it to talk to him. Rose stops the Dalek from exterminating van Statten, insisting that there must be something else that it wants, and after a moment, the Dalek admits that it wants its freedom. Rose accompanies it to the upper level of the bunker, where it blows a hole in the roof to reveal a shaft of sunlight. It does not understand Rose’s joyful reaction to the sunlight, as she had all but given up hope of ever seeing the sun again, and as it tries to understand, it opens up its battle armour to reveal the mutant inside, a pathetic, tentacled, one-eyed blob that paws feebly at the sunlight falling on its body.

The Doctor arrives and raises his gun, ordering Rose to step aside -- but she refuses, pointing out that the Dalek has held back from killing and is now basking in the sunlight. The Doctor realises that the Dalek is changing, and it finally sinks in that he’s changing too, into something terrible. The Doctor drops his gun in shock as he realises just how the destruction of his home and people has affected him. However, the Dalek can’t cope with the changes it’s experiencing; the Daleks believe themselves to be the supreme beings in the Universe, and since this Dalek is changing, that means it’s becoming something other than a Dalek. As it’s no longer a pure Dalek and it will never be human, the Dalek begs Rose to order its destruction, and she eventually does so, out of pity. Admitting that it is afraid at last, the Dalek closes up its battle armour and rises into the air. The Doctor and Rose watch from a safe distance as the bumps on the Dalek’s base separate from its armour, encircle it in a sphere of energy, detonate and shrink away to nothing. The last of the Daleks is dead.

In the aftermath, van Statten’s guards turn on him, blaming his selfishness for the death of over 200 personnel. Goddard orders them to erase his memory and dump him by the side of the road, just as he’s done to his own former employees. The Doctor and Rose return to the TARDIS, where the Doctor sadly ponders his status as the last survivor of the Time War; now he’s truly alone, apart from Rose. Adam follows to warn them that Goddard intends to close the base and fill it with cement, but as he prepares to return home, Rose tells the Doctor that Adam has always dreamed of seeing the Universe. The Doctor eventually gives in to Rose’s pleas and invites Adam aboard. Adam has no idea what he’s talking about, but when the Doctor and Rose enter the TARDIS, he follows them inside...