The Doctor, following a signal, lands the TARDIS half a mile under the Utah desert in a museum of alien artefacts. Whilst looking at the exhibits the Doctor trips the alarm when looking at the head of a Cybermen. Soon the Doctor and Rose are surrounded by soldiers and taken to Henry Van Statten's office.
Van Statten is a collector of alien artefacts. He has the help of Adam, a young English genius to locate the items. Adam is showing Van Statten an alien object when the Doctor suggests that they treat it more gently. The Doctor demonstrates the artefact, which turns out to be a musical instrument. This knowlegde impresses Van Statten, and whilst Rose stays with Adam, Van Statten takes the Doctor to see his one living specimen.
The specimen, named Metaltron by Van Statten, has been held in 'the Cage' for sometime. Van Statten's men have been torturing it, trying to get it to speak. The Doctor enters the cage, apologises for Van Staten's behaviour, and introduces himself. The metaltron awakes, and repeats the Doctor's name. The Doctor recognises the metaltron before the lights show what it really is: a Dalek.
The Dalek is powerless and bound, and the Doctor taunts it, telling it about the Time War, when all the Daleks, and the Time Lords, were destroyed. It is the last Dalek, and he is the last Time Lord. The Dalek screams for pity when the Doctor tries to electrocute it, and guards pull the Doctor away.
The Doctor tries to explain about the Dalek to Van Statten, and learns about how the Dalek fell to Earth over fifty years ago. Van Statten, learning that the Doctor is also an alen, has the Doctor scanned, whilst the Doctor tries to warn him about the Dalek, and what will happen if it ever gets out
Adam and Rose have been getting on well together, and Rose learns of his desire to visit the stars. Adam also tells Rose about the Dalek. When she sees it being tortured she gets Adam to take her to it. Feeling sorry for the Dalek, she reaches out to touch it.
The Dalek is able to extraploate and absorb genetic from Rose's DNA, and is able to regenerate itself. It manages to break free, and download the Internet, where it learns that it really is the last Dalek. The Dalek is able to drain the base's power in order to rebuild itself.
Van Staten releases the Doctor, and sends guards down to stop the Dalek. Their bulltes have no effrect, and the Dalek sets about killing the guards. Other guards attempt to set a trap for the Dalek, but the Dalek is able to levitate itself and set of the sprinkler systems. Water falls on the guards, and collects on the floor. One shot from the Dalek electrifies the water, killing the majority of the guards.
The Doctor reluctantly helps Van Statten to lower the bulkheads, trapping Rose inside with the Dalek. The Dalek fires at Rose, but is unable to kill her. The Dalek, appealing to the Doctor's emotions, threatens to kill Rose if he does not open the bulkhead. The Doctor agrees, releasing the Dalek to the upper level.
The Doctor finds an alien weapon in Adam's collection, and goes to confront the Dalek. However, combining with Rose's DNA has given the Dalek emotions it is not used to, and it begins to question itself. The Dalek needs orders, and asks Rose for a final order.
Rose does not want to give the final order, but she sees that the Dalek is in pain with the new emotions. She orders the Dalek to self destruct. Van Statten is ousted from command by his aide, Diana Goddard. The base is to be filled in with cement, and Adam tries to persuade the Doctor and Rose to leave before that happens. Rose tells the Doctor about Adam's desire to see the Universe, and he reluctantly agrees to let him on board.
