The ship soon lands and the two travellers find themselves on a windy hillside. The Doctor explains that it is the year 5,000,000,023 AD and the planet is New Earth. Both jubilant to be travelling again the pair run off across the grassy landscape, unaware they are being watched from an unknown location via a secret surveillance device disguised as a mechanical spider. The man observing them, a humanoid with patterned skin, is surprised yet grateful to find that the girl he sees on the screen before him is a pureblood human.
Meanwhile, the Doctor and Rose lament about their “first date” back on Platform 1. The Time Lord explains that when the original planet Earth was destroyed by its expanding sun the remains of the human race found a new world on which to live. Rose enquires as to the grand city that stands before them, some distance from the hillside. The Doctor identifies it as New New York.
In the surveillance area another unseen figure, a female this time, watches the pair on the hillside and recognises the girl’s face. She orders the spider to go closer and it listens as Rose asks the Doctor if they can visit the city. He explains they have another job to do first; someone is contacting him via the psychic paper telling him to come to Ward 26 of the nearby hospital.
The female watching them is Cassandra, whom the pair met before on Platform 1. After hearing that Rose is on her way to the hospital, Cassandra claims that soon she shall have her revenge on her for their last encounter.
The travellers enter the hospital via the foyer and find it filled with feline-like nurses, who busy themselves with their visitors and patients. Whilst the Doctor ponders why there is no gift shop in the hospital, Rose questions why disease has not been eradicated in the far future. The Doctor explains that as mankind advances across the stars disease advances with them, and then returns to his musings regarding the absent hospital shop.
Eventually abandoning this line of thought he enters a lift and tells it to take him to Ward 26. Rose rushes to join him but the doors close on her and she is forced to take another capsule. Despite asking it to take her to Ward 26 as well, Cassandra’s aide in the surveillance area overrides the controls and she instead descends to the basement. On the way both she and the Doctor are disinfected by the lift’s automatic cleansing system.
Arriving at their separate destinations the two friends step out of the lifts bone dry. The Doctor makes his way to Ward 26 whilst Rose tries to navigate the underground corridors. Cassandra’s aide, the man with pattered skin, greets her before running off. She gives chase, picking up a discarded metal bar as she goes. Meanwhile, in the upper levels of the building, Sister Jatt (one of the hospital’s cat nurses) escorts the Doctor around the ward. Both observing the patients surrounding him and attempting to sell the idea of setting up a small shop in the foyer to his guide, the Time Lord is fascinated by the many diseases and illnesses the nurses are treating, and takes great interest in their apparently advanced level of treatments and medicines.
His curiosity and suspicion abandon him as he identifies the familiar creature who has summoned him: the Face of Boe. Sister Jatt leaves him in the company of Boe’s carer, Novice Hame, and promises to check if Rose has been found anywhere. The Doctor kneels before the resting Face and Hame tells him that he is dying of an incurable disease: old age, having lived for thousands, possibly missions of years.
Down in the basement Rose emerges in the surveillance chamber, finding a film projector running in the middle of the room. The film playing is of a dinner party, and of the many guests in the movie Rose picks out the voice of one humanoid woman as sounding very familiar. She realises whom it belongs to and turns around to find Cassandra waiting for her. The no-longer humanoid sheet of skin introduces her new guest to her assistant Chip, a clone she modelled herself.
Rose asks her how she is still able to survive, having apparently died during their last encounter. Chip interrupts and explains that Cassandra’s brain survived the accident; he retrieved it and used the remaining skin from his mistress’ original body to reconstruct her. Now she is alone in the basement, relying on Chip to steal medicine with which to maintain her. She looks back at the film and recalls that it was the last time anyone called her beautiful.
Snapping out of her lamentation Cassandra explains to Rose that having spent so long in the hospital she has discovered certain secrets held by the cat nurses, and she wants to find out more. She asks Rose to come closer but instead she backs away, right into a trap. Chip pulls a lever on a nearby control panel and Rose’s arms are grabbed by two chains of light, emitted from nearby run-down machinery. Upon his mistress’ orders the clone then activates the “Psychograph”, causing a cage of light to descend on the trapped Earthling.
Suddenly Cassandra’s body disintegrates into a vapour trail, which floats toward Rose. It engulfs her and she falls down as the beams of light surrounding and binding her fade. Chip rushes over to awaken her and eventually Cassandra, now occupying Rose’s body, gets to her feet. After marvelling at once again having arms, fingers and hair she walks over to a nearby mirror and gasps in dismay.
“I’m a Chav!”
Up in Ward 26 the Doctor listens to Novice Hame, who explains that although largely inactive, the Face of Boe has been known to sing telepathically and transmit the songs into her head. She talks of the stories and legends surrounding the ancient creature, in particular the prophecy that moments before his death Boe will impart his final secret to one like himself – the wanderer, the man with out a home, the lonely God. The Doctor looks on in silence.
Cassandra continues to examine her new body before discovering her old brain has now decayed, now only her mind remains in Rose, whose own psyche is locked away in the depths of her consciousness. She does however manage to access some of the thoughts and memories contained in the suppressed intellect and discovers the man she saw Rose with on the hillside is the Doctor, only with a new face. Initially angered by the Time Lord’s hypocrisy, considering their previous encounter, Cassandra is surprised when Rose’s mobile phone begins ringing. She answers it, adopting a somewhat unconvincing cockney accent.
The caller is the Doctor, who is unaware that his companion has been possessed by his sinister former acquaintance. He tells her to come up to Ward 26 then hangs up, returning to the Duke of Manhattan, a patient who has been miraculously healed of a disease called Petrifold Regression. The Time Lord initially presumed the illness, which causes the victim to turn into stone, to be incurable, but somehow the nurses of the hospital have discovered an antidote. The Duke’s carer, Matron Casp, remains silent on the matter and is then called away by Sister Jatt, who explains one of their patients is conscious, and that poses a problem.
Cassandra meanwhile decides she must find out more about the secrets of the cat nurses, otherwise known as the Sisterhood. She takes a bottle of perfume from Chip and conceals it in her cleavage, then turns to leave.
Sister Jatt and Matron Casp arrive in a long dimly lit corridor lined with heavy metal doors that conceal glowing green chambers. They open one of the cells and examine the creature inside; and are surprised to find it has managed to develop speech patterns and free will. They close the cell door and walk away, casually incinerating the occupant before they go.
Rose, alias Cassandra, arrives in Ward 26 and is greeted by the Doctor, who explains to her the curiously innovative level of treatment in the hospital; pointing out several patients whose infirmities should take a long time to heal but are cured within a matter of days. The two of them leave the ward and make their way to an information screen, hoping to find the cause of such escalated medicinal care and the reason why the nurses have kept it a secret from the outside world.
After commenting on Rose’s curious new accent and then becoming the subject of a sudden outburst of affection from his companion, the Doctor browses the computer terminal for useful information but finds none. Cassandra tells him to search the subframe via the installation protocol and when he does so the section of wall before them slides away, revealing a long dark corridor. They make their way inside; unaware Novice Hame is following them.
The Doctor and Rose / Cassandra arrive in the same corridor Matron Casp and Sister Jatt visited moments before. They look out over a balcony opposite the line of cells and discover the secret section of the hospital is full of millions of similar cubicles. The Time Lord turns to open one of them and discovers a diseased human being inside. He closes the door and opens the next pod, in which another human is contained.
He explains to his companion that each subject has been infected with every known disease, and is being used as a test subject in order to find a cure. He warns her not to touch the creature inside, claiming if she does so the disease will spread. Cassandra asks how many patients there are in the complex and he tells her not only that there are millions of them, but also that they are not patients who visited the hospital; they were in fact born in the infirmary to be used for the sole purpose of experimentation.
Novice Hame appears in the corridor and tries to reason with the angered Time Lord, claiming the experiments are for the greater good. She explains that when mankind arrived on the planet they carried with them a large number of diseases, which had to be kept under control. The plague farm in which they stand was set up to combat the illnesses.
The Doctor remains outraged at the growth of so many humans for the sole purpose of inflicting disease upon them but Novice Hame remains unthreatened, deciding instead to question the authority with which the Time Lord criticises the hospital. He tells her simply that he is the Doctor; there is no higher authority.
Cassandra cuts in and asks if any of the humans in New New York know of this farm, and Novice Hame claims they do not. The Doctor, having realised something is wrong with his friend also turns to Hame for an answer, believing her and the other nurses to be responsible. She denies that they are guilty of harming Rose and after the Doctor insists she explain what has happened to his friend Cassandra cuts in, revealing her true identity. She removes the bottle of perfume from her person and sprays the Doctor with it, causing him to lose consciousness.
Novice Hame runs to fetch Matron Casp and Sister Jatt as Cassandra sets off a security alarm and hauls the Doctor into one of the empty pods, warning him that in a few minutes the inbuilt regulating system will inject him with every disease known to man. Eventually he awakens and orders her to relinquish Rose’s body, and she agrees to comply with his wishes – once she has found another one suitable for her to occupy.
Matron Casp arrives with Sister Jatt and Cassandra confronts them, threatening to reveal their secrets to the rest of the planet unless they give her a substantial amount of money. They refuse and so she switches to Plan B. She turns to Chip, who has arrived to help her, and tells him to unlock the pods. He does so and a line of cells is suddenly emptied, including the one containing the Doctor. A crowd of zombie-like patients begin to swarm the corridor, all begging to be saved from their infections. The Doctor, Chip and Cassandra manage to escape unharmed, leaving the nurses behind to fend for themselves.
The released patients manage to open the rest of the cells in the massive hidden complex before turning on the nurses. They stagger forward and one of them touches Sister Jatt, who is suddenly infected with their illnesses and drops down dead. Matron Casp runs to a nearby telephone and orders the hospital to be quarantined, and sure enough the entire building soon goes into lock-down. Meanwhile, some of the escaped patients turn to follow the Doctor, Cassandra and Chip, who are trying to make their way down to the basement. Others meanwhile make their way into the various wards and start infecting other patients and visitors.
Eventually Chip is separated from the Doctor and Cassandra and finds himself surrounded by infected patients. He manages to escape down a rubbish disposal chute whilst his mistress and the Doctor reach the basement. Once there the Time Lord orders Cassandra to leave Rose’s body, which she reluctantly agrees to, only to take over his instead. Rose recovers whilst Cassandra adjusts to her new body, noting the rhythm of the Doctor’s two hearts. They are found by the advancing patients, but manage to escape up a lift shaft. Meanwhile, Chip finds himself back in the plague farm, concealing himself in one of the pods to escape the diseased humans chasing him.
In the lift shaft Rose and Cassandra make their escape but are stopped when Matron Casp joins them on the ladder. She grabs Rose, believing her to have caused the chaos in the hospital, and as such to have destroyed its reputation. However, before she can act one of the patients, a group of who are now ascending the lift shaft as well, infects her and she plummets to her death. Rose and Cassandra manage to make their way to the top of the shaft where Cassandra is forced to return to Rose’s body so that the Doctor will be able to activate the Sonic Screwdriver and open the hatch at the top of the duct.
However, upon returning to consciousness the Doctor refuses to open the hatch unless Rose is released. Cassandra leaves Rose and re-enters him, but again her choice is met with protest. With danger fast approaching Cassandra concedes and enters the body of one of the patients. The Doctor then opens the hatch and he and his companion crawl into the corridor outside, but not before Cassandra escapes her new form and re-enters Rose.
After re-sealing the hatch the Doctor turns to Cassandra and again orders her to return his friend. She is not listening. Having spent time in the mind of one of the patients she has realised how lonely they are, just wanting someone to reach out and embrace them.
The Doctor offers her his hand and together they return to Ward 26. There the Time Lord formulates a plan to cure the infected patients and tells Cassandra and Novice Hame to collect all of the drip feeds for every known disease, which he then begins strapping to his jacket. He then returns to the lift shaft and leaps across the chasm to grab the cable. He attaches a botched zip line to it and prepares to descend to the cubicle far below.
Cassandra begrudgingly follows and grabs onto the Doctor’s back. He activates the zip line and they rapidly descend to the roof of the lift capsule on the ground floor. The Doctor opens up the container for the disinfectant system and begins pouring in all of the drip feeds. Cassandra remains on the roof, holding back the automatic release for the sprinklers inside the cubicle.
The Doctor opens up a hatch on the roof and jumps down into the lift. Once there he opens the doors to reveal a foyer full of infected patients. He beckons for them to join him in the lift and sure enough they approach. Some of them step inside and Cassandra releases the lever that sets off the disinfectant, allowing it to pour into the cabin below.
Within minutes the patients doused in the medicine are cured, and on the Doctor’s command begin moving about the foyer, passing on the cure to the other patients with a single touch. With every trace of disease is gone from the hospital, the Doctor declares that a new human race has been created, and that having helped create them Cassandra can no longer deny them, as she has done with many others in the past, believing herself to be the only true pure human being.
Some time later the police arrive and begin arresting the Sisterhood. The Doctor watches as Novice Hame is led away, and then hears a voice inside his head calling his name. He rushes back up to Ward 26 to find the Face of Boe waiting for him. Boe tells both the Doctor and Cassandra that recent events have renewed his lust for life, and then explains to them that although he does have a message for the Doctor, it can wait. He reveals that they will meet again, for one last time, and it shall be then that he imparts his secret.
He teleports away and the Doctor is left to compliment his absent friend on his enigmatic farewell. He then turns to Cassandra and claims it is time for her to leave Rose’s body once and for all, she has lived long enough; it is time to stop. At that moment Chip arrives, having survived the attack in the plague farm.
Cassandra realises her cloned servant will be willing to accept her mind and she swaps Rose for him. Upon gaining freedom, Rose collapses and the Doctor helps her to her feet, only for Cassandra to collapse moments later. She explains that Chip’s body will not last long, and admits that the Doctor is right; it is indeed time to die.
The Doctor realises there is one more thing he can do for Cassandra, and some time later he lands the TARDIS at the party Rose saw in the film playing in the basement. Cassandra, still in Chip’s body, exits the ship and approaches her former self. She tells her how beautiful she looks before collapsing in her arms. The younger Cassandra tends to Chip’s lifeless body as he slips away, ignored by the other partygoers.
Standing on the other side of the room Rose looks on, saddened by what she sees. She returns to the TARDIS, leaving the Doctor to watch the party alone.