School Reunion

Mr. Finch, the headmaster of Deffry Vale School, has been changing the school to improve the students' performance; his changes include free lunches with special chips. The Doctor, under the alias "John Smith", is undercover as a science teacher in the school and is shocked by the uncommon intelligence of the students. His companion, Rose Tyler, is working undercover in the school's cafeteria. Both the Doctor and Rose relate the mysterious events around the school to the chips: Rose observes that the chip oil has an adverse effect on the other kitchen staff, while the Doctor notes that the chips themselves are making children more intelligent.
The higher-than-average intelligence of the children has aroused media attention - in particular, the attention of investigative journalist Sarah Jane Smith. While at first the Doctor feigns ignorance, when Sarah Jane discovers the TARDIS during the night, he is forced to admit his identity. Sarah Jane meets Rose and Mickey, much to the chagrin of Rose. As they search the school, they find thirteen bat-like creatures asleep in Finch's office. Sarah Jane reveals a battered, inactive version of K-9, which - once repaired - identifies the chip oil as Krillitane oil. Rose, who was unaware he had past travelling companions and thought that she had "something special" with the Doctor, confronts him; he replies sadly that, while she can spend the rest of her life with him, he cannot spend the rest of his life with her.
The following day, the group returns to the school to investigate further. The Doctor confronts Mr. Finch, who confirms that he and the others are Krillitanes - a composite species that takes desirable attributes of the species they conquer. He attempts to subvert the Doctor, without success. Meanwhile, Sarah Jane and Rose try to unlock the programming on the school's computers; Mickey and K-9 remain in Sarah Jane's car for surveillance. With the Doctor's help, they discover that the computers - bolstered by the students' enhanced intelligence - are part of a Krillitane effort to solve the "Skasis Paradigm", a theory of everything. As the paradigm is nearly solved - which would allow the Krillitanes full control over time and space - the Krillitanes seal the school. Mr. Finch propositions the Doctor a second time, tempting him with the ability to save the Time Lords and override human mortality. With Sarah Jane's counseling, the Doctor refuses, and they run from Mr. Finch. Mickey crashes Sarah Jane's car through the school's doors and unplugs the computers, allowing the children to flee. The Doctor leads the Krillitanes to the kitchen; upon their arrival, K-9 opens fire on the oil barrels, destroying the Krillitanes, the school, and himself.
At episode's end, Rose, Sarah Jane, Mickey, and the Doctor are standing in the TARDIS. Sarah Jane declines a second chance of travelling in the TARDIS. Mickey says he would like to travel in the TARDIS instead, a suggestion of which Sarah Jane approves, much to the chagrin of Rose. She then asks Rose to stay with the Doctor and - if she needs help - to find her. Sarah Jane then gets a chance to part properly with the Doctor, who leaves her with a brand new K-9 as a parting gift.

Tooth and Claw

The Doctor attempts to take Rose to Sheffield in 1979 to see Ian Dury in concert, but ends up in the Scottish moors in 1879. They encounter a carriage carrying Queen Victoria, who has been forced to travel by roads to Balmoral Castle as a fallen tree has blocked the train line to Aberdeen, feared to be a potential assassination attempt. The Doctor poses as Dr. James McCrimmon using his psychic paper, and the Queen invites him and Rose to join her as they travel to the Torchwood Estate, a favourite of her late consort Prince Albert, to spend the night. The royal party is unaware that the Torchwood Estate has been captured by a group of monks from a monastery in St. Catherine's Glen led by Father Angelo, forcing its owner, Sir Robert MacLeish, to play into their ruse as they take the place of the house's servants and guards. The monks, having arranged for the fallen tree to force the Queen to the estate, have brought a man inflicted with a form of lycanthropy, hoping to pass its nature to the Queen and create a new "Empire of the Wolf".
The Doctor soon realizes the trap they have fallen into, and helps to save Rose, the Queen, and Sir Robert from Father Angelo's men and the werewolf by taking shelter in the estate's library, its wood coated with oil of mistletoe wood to stave off the beast. They study the library and discover evidence collected by Sir Robert's father, a polymath, and Prince Albert that indicate the werewolf is really the current form of an alien species that fell to earth in 1540 near the monastery, surviving by passing its lycanthropic form from human to human. The Doctor also realizes that the estate was designed as a trap for the werewolf, as by use of its strange telescope along with the Queen's Koh-i-Noor diamond, its cut fashioned by Prince Albert, they can force the werewolf to revert to human form and destroy the alien lifeform.Sir Robert sacrifices himself to allow the Doctor, Rose, and the Queen to prepare the telescope in the Observatory. They are able to trap the werewolf in the concentrated light of the full moon collected by the diamond. The transformed human being begs for the Doctor to kill him by increasing the power of the light concentration, which he obliges. As they recover, the Queen finds a small cut she believes came from a wood splinter, but the Doctor remarks to Rose that all her children will carry a form of haemophilia, and that perhaps this was simply a Victorian euphemism for lycanthropy. The next day, the Queen dubs the Doctor and Rose with royal titles before banishing them from the British Empire. The Queen is appalled and outraged by the unholy sort of lifestyle the Doctor and Rose share. In honor of Sir Robert's sacrifice and his father's ingenuity, she orders the creation of the Torchwood Institute to help defend England from further alien attacks.

New Earth

The Doctor uses the TARDIS to take Rose to the farthest point he's ever taken her, to the year five billion and twenty-three in the M87 galaxy. Humanity, after the destruction of the Earth, settled onto a very Earth-like world, called "New Earth", and Rose admires its beauty. The Doctor is summoned to "Ward 26" in a hospital in New New York through his psychic paper, and while he travels to the Ward, gets separated from Rose. In the Ward, the Doctor meets several humanoid feline nuns of the Sisters of Plenitude who are overseeing the patients, all who have incurable maladies but are somehow being cured by the Sisters. The Doctor recognises the Face of Boe, who reached out to "the Lonely God" in order to give him a message before he dies of old age. Meanwhile, Rose is brought to the basement of the hospital, where she is escorted by Chip to meet Lady Cassandra, who has survived from her previous encounter with the Doctor and has been watching the two since they arrived. Chip has been using the hospital facility to care for Cassandra, but Cassandra is suspicious of the methods used in the hospital and requires Rose's help. Rose tricked into stepping into a "psychograft" machine that allows Cassandra to implant her mind into Rose's, leaving her old "body" to die. Cassandra can read Rose's thoughts, and knowing of the Doctor's new form, goes to meet him as "Rose". The Doctor is suspicious of "Rose"'s actions, such as kissing him passionately or having knowledge of the advanced computer systems, but is more concerned on how the hospital can cure the incurable. He and "Rose" discover that the hospital houses hundreds of pods containing artificially-grown humans, forcibly inflicted with numerous diseases, such that the Sisters can discover their cures. The Doctor accuses the Sisters of the atrocity, though they insist it was necessary to deal with the influx of patients. The Doctor, believing that Rose's current actions are also a result of being a test subject, is suddenly knocked unconscious by a perfume gas and wakes up locked in one of the pods. "Rose" then approaches the lead Sister, Matron Casp, demanding payment for her to keep quiet about the hospital secrets, and when she is refused and threatened physically, releases the Doctor and some of the humans as a distraction, but the infected humans further release the others, and a zombie-like attack begins, with those infected trying to attack anyone healthy.
The hospital is put into quarantine as the Doctor, "Rose", and the remaining Sisters try to flee the lower levels. To help their escape, Cassandra is able to jump her mind between other bodies, including one of the infected humans, before jumping back to Rose, and learns that those humans feel a strong sense of loneliness of not being able to touch or be touched. Eventually, the Doctor and "Rose" reach Ward 26, and grab all the intravenous medical solutions; emptying them into a disinfectant shower, they are able to spray the mixture onto a group of the infected humans, who within moments become cured of their diseases. The Doctor encourages them to go and spread the cure to the other infected people, and soon, the attack is over. The police arrest the surviving Sisters, while the Face of Boe, who has also been cured, tells the Doctor that the message for him can wait until they meet for the third and final time, and then teleports away.The Doctor now orders Cassandra out of Rose's body. Cassandra transfers her consciousness to a willing Chip instead, but his cloned body begins to fail, and Cassandra accepts her impending, true death; the New Earth has no place for people like her and Chip. The Doctor does one last thing for Cassandra, taking her back to see herself on the last night someone had called her beautiful. "Chip" approaches the Cassandra of the past and tells her just that, and collapses into the younger Cassandra's arms as she comforts "him". As the older Cassandra finally dies, the Doctor and Rose silently leave in the TARDIS.