The TARDIS materialises in a dark warehouse in 2012, many storeys below the surface of Utah near Salt Lake City, in what appears to be a museum of alien artifacts... including a Cybermen head and a Slitheen arm. The Doctor (Christopher Eccleston) touches one of the cases which sets off the alarm, and soon he and Rose (Billie Piper) are surrounded by guards who take them prisoner.

The facility they are in is owned by Geocomtex, a technology company owned by the wealthy and powerful Henry van Statten (Corey Johnson), who arrives in a helicopter at the complex and meets its manager, Diana Goddard (Anna Louise Plowman) and a brainy science genius who examines the alien technology, Adam (Bruno Langley). The Doctor and Rose meet van Statten, who remains unimpressed with the Doctor's seemingly endless knowledge of alien technology. But van Statten realises the Doctor may have some use to him, as he puts him into a cell with Geocomtex's one live alien specimen... what he calls a "metaltron," but what the Doctor soon realises is a Dalek. A Dalek that should not exist.

The Doctor informs the Dalek of recent history, where at the end of a massive Time war, the Daleks and the Time Lords fought and destroyed each other; both he and the Dalek are the last of their kind. The idea infuriates the Doctor and changes the Dalek's perception, but the Doctor soon attempts to electrocute the Dalek. Van Statten stops him, and strings him up to interrogate him, scanning the Doctor and recognizing he's an alien. Rose, meanwhile, gets to know Adam, who does much of the research at the base and years to go to the stars, but soon persuades him to let her see the captive Dalek. Rose meets it, and feels pity for it... but when she touches the Dalek, it samples her DNA, allowing it to recharge itself and escape. Suddenly, the Dalek is loose and the base is under full alert; it kills the security officer, Bywater (John Schwab) and his entire squadron, and heads toward the main complex.

Adam and Rose flee into the stairwell, while the Dalek kills a soldier, De Maggio (Jana Carpenter), who tries to stop it. Up on the surface, van Statten, Goddard and the Doctor attempt to find safe passage out of the underground for Adam and Rose. The two meet up with another security contingent, but the Dalek outwits its commander and the team when it activates the fire safety sprinklers and then electrocutes everyone through the water. Adam and Rose flee upward as the Dalek levitates to follow them; Adam makes it to safety, but before Rose is able to get through the bulkhead, the Doctor is forced to close it. The Dalek takes her prisoner, but for some reason doesn't kill her.

The Dalek tries to use Rose as leverage; it almost attacks van Statten and Diana but then stops, and takes Rose to the top floor, where it appears it will attempt to escape. However, the Dalek is transfixed by the sunlight shining on it through the roof; Rose's DNA has not only reactivated it, but begun to change it completely. The Doctor arrives with a weapon Adam helped him find, but Rose pleads for the Dalek, who has opened its casing and allowed the light to penetrate the mutated creature inside. The Doctor tries to stop his own instincts, but the Dalek pleads with Rose for one last order - to kill itself. Rose gives in, and the Dalek commits suicide.

As van Statten prepares to leave, Goddard ambushes him, having him escorted away to have his brain wiped clean of memories in punishment for all the death he's caused; she'll have the entire base filled with concrete and destroyed. The Doctor and Rose return to the museum to reenter the TARDIS, but Rose has dragged Adam along, asking the Doctor if he can travel with them to see the stars he's always imagined. The Doctor protests, but Adam enters the TARDIS before it departs for another adventure, now with a party of three aboard...