The Doctor learns from the Ood that the Master will shortly return, but that there is something else emerging from the darkness that will lead to "the end of Time itself". As the Doctor races to Earth, a cult loyal to the Master perform a resurrection ritual, using the Master's genetic material from Lucy Saxon's lips to complete the process before offering their lives to the revived Master. Lucy, aware of the Master's failsafe, introduces a fatal component to the ritual, destroying herself and everyone else in the prison. The Master escapes, having gained supernatural agility and telekinetic powers from the failed ritual that drain him of his life energy, making him suffer from constant hunger.
The Doctor arrives on Earth on Christmas Eve and begins to trace the Master. He encounters Wilfred Mott, who reveals that he has been having nightmares and worries for the Doctor; the Doctor explains to Wilfred of the regenerative abilities of Time Lords and the prophecies of his death about the man that will "knock four times". The Doctor tracks the Master to wastelands outside of London, but the Master subdues him and forces him to listen to the sound of drums in his head. The Doctor realises the sound is not a figment of the Master's insanity, but before he can learn more, elite troops under billionaire Joshua Naismith's employ abduct the Master.
The Doctor returns to Wilfred the next day, who is able to help identify Naismith's involvement with a book gifted to him by Donna Noble. Wilfred retrieves his old service pistol after being warned by a mysterious woman in white before joining the Doctor in his TARDIS and travelling to the Naismith's estate. There, they discover Naismith has recovered an alien device called the "Immortality Gate" and has enlisted the Master to correct its programming in order to grant Naismith's daughter immortality. The Doctor and Wilfred reveal two of the technicians as Vinvocci aliens working undercover to retrieve the device themselves, but fail to understand the Doctor's concern when they tell him it is a simple medical device designed to heal the population of an entire planet.
The Doctor is too late to stop the Master from completing the programming, breaking free of his bonds, and jumping into the gate. The process turns every human—save for Wilfred whom the Doctor protected in one of the isolation booths for the Gate and Donna due to her half-Time Lord nature—into clones of the Master, supplanting the human race for the literal "Master Race". The victorious Master and his doppelgangers taunt the Doctor, who can only look on in horror, at his loss.
Far across the Universe, the narrator remarks that the Master's removal of humanity is only the beginning of far greater events. Revealed to be the Lord President of the Time Lords, he addresses a vast chamber full of other Time Lords, and announces that it is "the day the Time Lords returned. For Gallifrey! For victory! For the end of Time itself!"
Part Two
The Doctor and Wilfred escape from the Master with the help of the Vinvocci, taking refuge on their orbiting ship. The Time Lord President has engineered events, first by placing the sound of drums in the Master's head as a young child, such that when amplified by the billions of clones, would act as a signal to the Master in the present. The President has also sent a Whitepoint star diamond to Earth that can boost the signal and lock onto its source. Through these, the Time Lords are able to create a link to the Master to let them escape from the Time Lock placed on the Time War.The President and his council materialise in the Gate room. The Master attempts to reuse the Gate to transform all Time Lords into copies of himself, but the President stops the attempt and reverses the transformation of the human race. At the same time, Gallifrey begins to materialise above Earth, along with all the other horrors created in the Time War. The President reveals that now free of the Time Lock, the Time Lords plan to end time, destroying the universe and allowing them to evolve into a higher form of consciousness. The Doctor, long aware of the Time Lords' plan, is forced to return to Earth, armed with Wilfred's gun. As he struggles over killing the Master or the President, either action severing the link, the Doctor catches the glimpse of one of the women on the Time Lord council—the same woman in white that Wilfred has seen and who was against the Time Lords' return. The Doctor recognises her, and, inspired, shoots the Whitepoint star diamond. As the Time Lords are drawn back into the Time Lock, the President attempts to kill the Doctor, but the Master intervenes, sacrificing himself to gain revenge on the Time Lords for tormenting him all his life. In a flash of light, the Time Lords, the Master, and Gallifrey have all disappeared.
Taking a moment to realise his victory, the Doctor hears four knocks, the sound which precedes his death. He finds Wilfred, having returned to help the Doctor, still trapped in the Gate's isolation chamber that will be flooded with radiation due to the Master's modifications; only the self-sacrifice of another will free him. The Doctor releases Wilfred, collapsing in agony as he receives a massive dose of radiation.
Although he survives initially as his body absorbs the radiation, the healing of the Doctor's wounds shows his regeneration has started. He returns Wilfred home, and visits several of his past companions. Martha Jones is married to Mickey Smith; the Doctor saves them from a Sontaran. The Doctor prevents Luke Smith from being hit by a car. Luke points him out to Sarah Jane; she and the Doctor silently say their goodbyes. At an extraterrestrial bar, the Doctor passes a note to Jack Harkness, encouraging him to start a conversation with Midshipman Alonso Frame ("Voyage of the Damned"), seated next to him. The Doctor attends a book-signing by Verity Newman, the great-granddaughter of Joan Redfern ("Human Nature" and "The Family of Blood"), for her book A Journal of Impossible Things based on Joan's diaries; the Doctor asks Verity if Joan had been happy in the end, to which she returns the same question to him. The Doctor attends Donna's wedding, giving Wilfred and Sylvia Noble a winning lottery ticket for Donna, bought with money borrowed from Sylvia's deceased husband Geoff in the past, to allow Donna and Shaun to live happily. The Doctor finally visits Rose Tyler on New Year's Day 2005, the year when she meets him as the Ninth Doctor, and tells her she will have "a great year".
The Eleventh Doctor examines his new features
Continuity
At the start of "Part One" the Doctor explains his delay to Ood Sigma. Among his various adventures, he mentions having married "Good Queen Bess" and refers to her nickname, 'The Virgin Queen'. At the end of "The Shakespeare Code" Queen Elizabeth appears infuriated at seeing The Doctor (calling him her sworn enemy); he does not recall meeting her and presumes he will meet her in his future.[5][6][7]During "Last of the Time Lords", an unknown woman's hand is seen collecting the Master's ring from the pyre once it is cold; this scene is revisited, showing the woman to be a member of the Harold Saxon cult, and who uses the ring to resurrect the Master.
In the café, Wilfred Mott reminisces about his adventures with the Doctor in "The Sontaran Stratagem" and "The Stolen Earth". Donna's returning memories at the end of Part One include images of Davros from "Journey's End", the Vespiform ("The Unicorn and the Wasp"), the Ood ("Planet of the Ood"), the Sybilline High Priestess ("The Fires of Pompeii") and the Empress of the Racnoss ("The Runaway Bride"). When Donna is surrounded by clones of the Master, she unconsciously emits a wave of energy that knocks herself and the other Masters out; the Doctor refers to this as a "self-defence mechanism" he put in place when he altered her mind at the conclusion of "Journey's End".
The Doctor, on seeing the appearance of the Vinvocci, green-skinned aliens with spikes on their heads, comments on his previous encounter from "Voyage of the Damned" with Bannakaffalatta, a red spiky-headed being. The Vinvocci are quick to differentiate themselves from Bannakaffalatta's race, the Zocci.
Joshua Naismith states that he acquired the Immortality Gate after the fall of the Torchwood Institute.
The Doctor hides the TARDIS from the Master by putting it "one second out of sync" with the rest of reality. Davros used the same technique to hide the 27 stolen worlds in "The Stolen Earth".
The Time Lord President compares two dissident Time Lords to the Weeping Angels as he shames them. In "Blink", the Doctor described the Weeping Angels as being "as old as the universe, or very nearly, but no one really knows where they come from." One of the monsters the Doctor mentions as returning from the Time Lock is the 'Nightmare Child', which was previously mentioned in "The Stolen Earth" as having devoured Davros.
One of the two dissident Time Lords, described as "The Woman" in the credits, visits Wilfred on several occasions, appearing and disappearing in unexplained ways. When she lowers her arms to stare at the Tenth Doctor he appears to recognise her, but when later asked by Wilfred about her identity, the Doctor evades the question. British newspapers The Daily Telegraph and The Daily Mail identified the character as the Doctor's mother as early as April 2009.[8][9] Russell T. Davies wrote in an email to the author of The Writers Tale, "I like leaving it open, because then you can imagine what you want. I think the fans will say it's Romana. Or even the Rani. Some might say that it's Susan's mother, I suppose. But of course it’s meant to be the Doctor’s mother."[10]
The Doctor at one point addresses the Lord President as "Rassilon", the name of the founder of Time Lord society from the classic series, although the character is only identified in the credits as 'The Narrator / Lord President'. In the accompanying episode of Doctor Who Confidential, Russell T Davies stated that the character's name was indeed Rassilon.[11]
When Mickey Smith and Martha are shown on the run from a Sontaran before the Doctor's appearance, Mickey mentions that this is "no place for a married woman" until Martha counters with "then you shouldn't have married me." The end credits note her name as Martha Smith-Jones.
At the extraterrestrial bar where the Doctor meets Jack, there are several previous aliens from the series present, including the Graske, Raxacoricofallapatorian, Adipose, Hath and Judoon. The song heard playing during this scene is "My Angel Put The Devil in Me" from "Daleks in Manhattan", which appeared on the soundtrack for the third series.
Verity Newman is played by Jessica Hynes, the same actress who played Joan Redfern in the episodes "Human Nature" and "The Family of Blood". The name "Verity Newman" is based on Doctor Who creator Sydney Newman and the show's first producer, Verity Lambert.[12] Professor John Smith averred that his parents were Verity and Sydney. A pocket watch featured prominently in the plot of both Hynes's original episodes, and a pocket watch is featured on the cover of Newman's book.[12]
After regenerating, the Eleventh Doctor is disappointed that he is "still not ginger", referring to the Tenth Doctor's comment "Aw, I wanted to be ginger... I've never been ginger!" in "The Christmas Invasion". This line was a source of complaint for some viewers, leading the BBC to issue a statement clarifying its intent.[13]
During the period between his exposure to the radiation and his eventual regeneration, the Doctor is shown visiting his past companions, as well as the granddaughter of a woman he once fell in love with. Afterwards, the comic strip "Lucky Heather" in Doctor Who Adventures magazine indicated that he also visited his comic strip companions Heather McCrimmon and Wolfie Ryder. Ultimately, a 2010 episode of The Sarah Jane Adventures entitled Death of the Doctor reveals that the Doctor actually visited virtually all of his past companions during this time, including Jo Grant, whom he had known during his third incarnation.