Voyage of the Damned

The episode continues from the end of the third series finale "Last of the Time Lords", when the TARDIS collided with the Titanic. To investigate further, the Doctor runs the TARDIS's self-repair programme and boards the Titanic, where he discovers that the "ship" is an interstellar cruiser from the planet Sto.
Modelled after the Earth ocean liner of the same name, the ship is orbiting present-day Earth to observe "primitive cultures"–specifically, Christmas. He decides to stow away, only telling waitress Astrid Peth. The Doctor joins Astrid on a brief excursion to Earth, along with married couple Morvin and Foon Van Hoff, an alien with a spiked red head named Bannakaffalatta, and historian and guide Mr Copper. However, the populace of London fled in fear of a third consecutive extraterrestrial attack, and only a few people remain in the city, most notably a newspaper seller called Wilfred Mott.
After the party return from the excursion, the ship's captain, Hardaker, dismisses all the bridge officers to commit an act of sabotage; Dropping the vessel's protective shielding he magnetises the hull of the ship, causing meteors to collide with it, hitting the vessel at three points along the starboard side. The resulting collision kills most of the passengers on-board and puts the vessel at risk of causing an extinction level collision with Earth due to its nuclear powerplant. The Doctor makes contact with Midshipman Alonzo Frame, a crew member who survived the collision, who although suffering from a gunshot wound helps him stabilise and maintain power from the damaged engines. Midshipman Frame had previously refused to leave the bridge, citing company regulations that under no circumstance should the bridge be held by a single officer.
En route to the bridge, the Doctor's party are repeatedly attacked by the Host, androids resembling angels who were programmed to kill survivors of the collision. The Doctor breaks from the party and attempts to reach the control point for the Host. He is taken to the Host's leader, former cruise line owner Max Capricorn. He was bitter about being forced out of his own company and plotted the Titanic's inevitable collision with Earth to bankrupt the company. To save the Doctor, Astrid rams Capricorn with a forklift. Astrid and Capricorn ride off a precipice to their deaths.
The Doctor uses the Host to reach the bridge, where he uses the heat from entry into the Earth's atmosphere to start the ship's auxiliary engines, the primary Nuclear Storm Drive having shut down. After stabilising the ship, narrowly avoiding a collision with Buckingham Palace, the Doctor realises that the teleport bracelet Astrid was wearing backed-up her molecular pattern. However, the damaged system can only partially regenerate Astrid. The Doctor reluctantly allows her to dissipate into atoms, so she can fulfil her dream of exploring the universe. The party then amicably part ways, vowing not to forget the Doctor's and Astrid's actions. Mr Copper is left on Earth by the Doctor, since the ensuing investigation is bound to reveal his fraudulent position.

Last of The Time Lords

A year after the appearance of the Toclafane, the human population is on the verge of extinction. After escaping from the Valiant, Martha Jones has been traveling across the Earth for a year, staying out of the Master's detection through use of the TARDIS key acting as a perception filter. She returns to England with help of a former doctor Thomas Milligan, and seeks Professor Docherty to help her capture a Toclafane.
Using data gathered when a Toclafane was hit by lightning, Professor Docherty is able to recreate the conditions, and the three are able to stun one of the beings. When they open it up, they discover that the Toclafane are humans from the year 100 trillion, who, having attempted to reach Utopia and finding nothing but darkness, became insane in their search to outlive the universe and cannibalised themselves to become the child-like bio-mechanical Toclafane, brought to the present through the Doctor's TARDIS and the Paradox Machine in order to avoid a temporal paradox. Armed with this information, Martha announces that she will face the Master, armed with a special gun created by Torchwood and UNIT that can stop a Time Lord's regeneration, giving her a way of defeating the Master. After Martha and Thomas leave, Professor Docherty, desperate for any information on her son, reports Martha's presence to the Master.
Martha and Thomas meet up with several other human groups hiding in shelters, and tells tales of her travels in the last year. The Master along with his men land and begin to round up the humans, seeking Martha and demanding she hand over the gun. After she does so, the Master destroys it, then attempts to kill her, but Thomas sacrifices himself to save her. The Master realises that killing Martha in front of the Doctor would be more satisfying, and brings her back to the Valiant. There, Martha learns that the Master has kept the aged Doctor as a pet and even further humiliating him by aging him further and putting him into a bird cage, while he has kept Jack in chains, killing him and forcing him to revive repeatedly. The Master reveals that he is moments away from launching Toclafane fleets from Earth to conquer the rest of the universe, and forces Martha to kneel in front of him. However, the fleet fails to launch at the end of the countdown, confusing the Master.
Martha reveals that she was not travelling on Earth to locate the fictional anti-regeneration gun, but instead to tell people of the Doctor and send their thoughts to the Doctor at the fleet's launch moment; with their emotions, the Doctor is able to use the Archangel network to collect the vast amount of psychic energy and use it to restore his body and ends the Master's control. As the Master cowers, the Doctor says the words that the Master was most afraid to hear: "I forgive you". As Martha, Jack and the others fight to keep the Toclafane from defending the Paradox Machine, the Master teleports himself and the Doctor to Earth using Jack's vortex manipulator and threatens to detonate the fleet and destroy Earth in the process, but the Doctor calls his bluff, reminding the Master that doing so will kill him – the one thing the Master is incapable of – and is able to make the Master surrender. The two return to the Valiant just as Jack and other soldiers destroy the Paradox Machine, causing time to rewind just before the rift opened; those on board the Valiant are still aware of the events of the last year.
As everyone recovers back on Earth, Francine Jones attempts to shoot the Master, but the Doctor is able to persuade her not to do so. However, they are caught off-guard when Lucy Saxon kills him herself. The Master, dying in the Doctor's arms, refuses to regenerate as to be a prisoner for the rest of his life. As the Doctor desperately pleads to the Master to stay alive, the Master gives his final words, "I win", and dies, sending the Doctor into an emotional turmoil. Later, the Doctor burns the Master's body on a pyre, but an unseen woman's hand later recovers his signet ring from the ashes.
The Doctor drops off Jack in Cardiff to rejoin his team, deactivating his vortex manipulator to prevent Jack from jumping around time and space. As Jack departs, he reflects on his immortality and what he might look like in a million years, and notes to the Doctor and Martha that in his youth on the Boeshane Peninsula, his good looks earned him the nickname "the Face of Boe". Martha takes her leave of the Doctor, opting to look after her family and finish her medical degree, recognising that while she loves the Doctor, he cannot return that; Martha however gives him a cell phone so they can stay in touch and travel again one day. As the Doctor pilots the TARDIS away, now with his severed hand aboard, it is struck by a large force and the bow of a ship called the Titanic bursts through a wall of the control room, leaving the Doctor perplexed how that could occur.

The Sound of Drums

The Doctor, Martha, and Jack manage to escape from Futurekind in the year 100 trillion through Jack's repaired Vortex Manipulator, finding themselves in London. They quickly learn that the Master has taken on the persona of "Mr. Harold Saxon", the current Prime Minister, using his Archangel phone network to subliminally influence the population into voting for him while masking his presence from the Doctor. The three narrowly avoid a bomb placed in Martha's flat, and the arrest of Martha's family, before the Master contacts them to gloat about his seeming victory.
The Doctor learns that the Master was resurrected by the Time Lords to fight in the Time War to be the perfect warrior, but instead the Master fled to the end of the universe and made himself human when defeat seemed inevitable. The Master reveals that the three are now England's most wanted criminals and has stripped them of any help, including sending Jack's Torchwood team on a wild goose chase to the Himalayas. Hiding in an abandoned building, the Doctor uses parts of Martha's laptop and the TARDIS keys to create a perception filter so they can move about unnoticed. He explains some of the Master's past: that as a child, the Master looked into the Time Vortex, and was likely driven mad as a result. They come to discover that the Master, as Saxon, is planning to reveal Earth's first contact the next day with an alien race known as the "Toclafane", (in truth, the name 'Toclafane' refers to the Gallifreyan equivalent of the "bogeyman",) and the Doctor insists they must be present.
As the appointed time of first contact nears, United States President-Elect Winters arrives in England and places the operation in the hands of UNIT, transferring the meeting aboard the flying aircraft carrier, the Valiant; the Master accepts this change, as it suits his purposes, and along with his wife Lucy and the rest of Martha's family, board the vessel. The Doctor, Martha, and Jack teleport aboard with Jack's vortex manipulator, discovering the Doctor's TARDIS has been "cannibalised" by the Master to create a Paradox Machine which is building up power to be activated at the appointed time of first contact.
As the three make their way to the bridge, the Doctor tells them to try to get their perception filter around the Master to reveal who he really is to humanity and stop his plan. As they enter the bridge unnoticed, the first four Toclafane, floating metal spheres, appear on the bridge and demand to see the Master; the Master delightedly reveals himself and orders the Toclafane to kill Winters. The Master then reveals that he is well aware of the Doctor's presence in the room by using his laser screwdriver upon the group, temporarily killing Jack while aging the Doctor by 100 years through the use of LazLabs genetic manipulation technology using biological data from the Doctor's severed hand that the Master had stolen. Jack gives Martha his vortex manipulator and tells Martha to get off the Valiant, as there is no way they can defeat the Master.
The Master brings Martha's family into the bridge as the Paradox Machine nears activation, and taunts the aged Doctor about the nature of the Toclafane and his victory. The Paradox Machine activates as the Master tells the people of Earth that it's the "end of the world" and plays the song "Voodoo Child". A massive rift opens above the Valiant, and six billion Toclafane descend from it. The Master orders the Toclafane to "remove one tenth" of the Earth's population. As Martha tends to the aged Doctor, he whispers into Martha's ear. Martha, unable to save the Doctor, Jack, or her family, promises she will return, and uses Jack's vortex manipulator to teleport off the Valiant to find safety on Earth; she then flees into the distance as the Toclafane wreak havoc on humanity. The Master himself gloats about the fall of the human race and forces the Doctor to look upon his "new dominion as Master of All."

Utopia

The TARDIS lands in Cardiff to refuel from the Rift. The Doctor states that this will only take twenty seconds (in contrast to his previous visit), noting that the Rift has been active recently. Captain Jack Harkness races towards the TARDIS, grabbing onto it as it dematerialises, causing it to hurtle out of control to the end of the Universe.
After landing in the year 100 trillion on the planet Malcassairo, Jack confronts the Doctor about abandoning him on Satellite 5, and asks about Rose Tyler. Jack reveals that he returned to Earth using a vortex manipulator, but was stranded in the 19th century; therefore, he went to wait at the Cardiff Rift, knowing the Doctor would eventually come back. Exploring, they find a dead city and encounter the Futurekind, cannibalistic humanoids who are hunting a human. The human is attempting to reach a transport to "Utopia", the last hope of the human race.
At the transport site, the TARDIS crew meet the elderly Professor Yana and his insectoid assistant Chantho, who are desperate for help. The spacecraft to Utopia can't launch due to problems with its experimental engine system. Despite the unfamiliar technology, the Doctor solves the scientific problems, and Jack makes final preparations in a heavily irradiated room. As Jack does this, he and the Doctor discuss Jack's inability to die, saying that his resurrection is why the Doctor abandoned him on Satellite 5. The rocket finally takes off for Utopia, leaving the Doctor, Yana, Chantho, Martha, and Jack behind.
A separate plot shows that Yana has been hearing a constant drumbeat inside his head — a condition he reports having had all his life, with the drums getting louder of late. Words such as "regeneration" and "TARDIS" — elements of Time Lord lore — exacerbate the problem. When Martha expresses concern over the Professor's uneasiness, he reveals a long-standing concern with time, and shows Martha a broken fob watch he's had since obtaining it as a child, identical in design to John Smith's watch in "Human Nature" and "The Family of Blood". Concerned about the implications, Martha rushes to inform the Doctor.
When the Doctor hears about Yana's timepiece, a flashback sequence inter-cut with the letters of the Professor's name makes clear that "Yana" is an acronym of "You are not alone", the Face of Boe's last words to the Doctor. At the same time, Yana opens the watch, releasing his Time Lord essence. Frantic and horrified, the Doctor races towards Yana's laboratory but is hindered as the Professor closes the doors and allows the Futurekind to enter the base. Yana reveals his true identity to Chantho: he is the Master. He electrocutes her, but Chantho manages to shoot him before dying.
The Doctor arrives in Yana's laboratory just as the Master enters the Doctor's TARDIS, taking the severed hand (which Jack recovered after the events of "The Christmas Invasion" and had carried ever since) with him. He then deadlock seals the TARDIS doors, preventing the Doctor from opening it. Dying from Chantho's shot, the Master regenerates into a younger body, whose voice Martha recognises. After taunting and berating the Doctor, he leaves in the TARDIS, stranding the three time travellers in the distant future, with the Futurekind about to break through the door.

Blink

In 2007, Sally Sparrow enters the dilapidated house, Wester Drumlins, to look for subjects to photograph but instead finds eerie angel-like statues, a Yale key hanging from one of their hands, and messages from "the Doctor" behind the peeling wallpaper addressed to her, warning her of the "Weeping Angels". Sally returns the next day with her friend Kathy Nightingale to explore further; Kathy disappears as at the same time a young man claiming to be Kathy's grandson delivers a letter to Sally. The letter from Kathy explains, just moments ago from Sally's perspective, Kathy suddenly found herself in the 1920s in Hull, settling down with a husband and leading a peaceful life, and requests Sally to let her closest relative, her brother Larry, know of her disappearance.
Sally visits Larry at a DVD rental store, and finds that he has documented a series of "easter eggs" across seventeen unrelated DVDs, each with the same man calling himself "The Doctor" having half of a conversation with the viewer. Larry gives Sally a list of the DVDs as she leaves for the police station. There, she meets Detective Inspector Billy Shipton, who explains that there have been several disappearances at the Drumlins, and shows her an impound lot containing vehicles abandoned near the Drumlins, including a locked fake police box. Sally leaves, but remembers the key she found, and returns to find Billy has disappeared. She immediately receives a call from a much older Billy at the hospital and visits him. Billy explains after she left he found himself facing the Angels who were trying to retrieve the police box. Billy then suddenly found himself in 1969 and met the Doctor, who asked him to relay a message to Sally decades later; Billy subsequently married and started a video production house and was responsible for putting the easter eggs on the DVDs. Before Billy dies, he tells Sally the Doctor's message to her: to look at the list of DVDs. Sally discovers that the list is her own DVD collection, and realises the easter egg is meant for her.
Sally and Larry return to the Drumlins with a portable DVD player, and watch the entirety of the easter egg. Sally discovers she can converse with the Doctor as, in the past, he possesses a complete version of the transcript that is currently being compiled in the present by Larry as he watches. The Doctor explains that he and Martha Jones were transported to the past by the Weeping Angels, beings that feed off the potential time energy of others. The Angels are "quantum locked", allowing them to move incredibly fast when unobserved but cannot move when watched, and thus warning Sally not to blink when they are around. The Doctor tells them they are seeking his TARDIS to acquire its potential power which could be catastrophic. When the Doctor comes to the end of the transcript, Sally realises Larry has stopped writing it due to the presence of an Angel in the room, and the two quickly escape to the basement. There, they discover the Angels have brought the TARDIS, and Sally and Larry take shelter inside it as the Angels surround them. Inside they learn that the DVD can be used to activate the TARDIS; upon doing so the TARDIS dematerialises, leaving the two of them behind. However, with the TARDIS gone, the Angels have been tricked into observing themselves, permanently frozen as statues staring at each other.
A year later, Sally and Larry have become romantically involved opening a DVD and book store together, though Sally's insistence on keeping a folder of the events for the Doctor worries Larry. As Larry steps out for an errand, Sally sees the Doctor and Martha hurriedly leave a taxi in front of the shop, carrying a bow and quiver of arrows, and goes to meet them. When they do not recognise her, she realises that they have yet to experience the events that sent them to the past, and hands over her folder of information, warning the Doctor he may need it in his future and completing the ontological paradox. The Doctor and Sally say their goodbyes as Larry returns, surprised to see the man from the easter egg. Sally and Larry return to the shop hand in hand. The episode ends with a repeat of the Doctor's warning to Sally, this time directed at the viewer, overlaid with flashes of famous bronze and stone statues.

The Family of Blood

The Family of Blood, in the form of the humans they have possessed, hold Martha and Joan Redfern captive at the village dance; demanding that John Smith—the Doctor's human form—make a choice about which of the two to save. As John tries to decide, Timothy Latimer, in possession of the Doctor's fob watch containing the Time Lord persona, briefly opens it up again (terrifying the Sister with an image of the Doctor at his most cruel and merciless), which is detected by the Family and momentarily distracts them, allowing John, Joan, Martha, and the other villagers to escape, collecting at the school. John helps to organise the school's defenses while Martha and Joan search for the fob watch.
The Family assault the school with an army of scarecrows, but the boys in the school are able to defend the first wave. When the Family attempts to show John that they have discovered his TARDIS, Joan, having seen the images of the TARDIS in John's "Journal of Impossible Things", realises that John is really the Doctor. As the Family continues to assault the school, John, Joan and Martha escape to the cottage of the little girl's family which the Family had possessed. Realising that the Doctor has left the school, the Family returns to their ship and begins an aerial bombardment of the village. As John and the others take shelter, Tim arrives and returns the watch to John, and both Martha and Joan implore John to use it to become the Doctor and save everyone. John is hesitant as using the watch is the same as committing suicide. Joan takes John aside and shares a series of images generated by the watch showing what their lives may have been like in the future, happily settling down, raising a family, and growing old together. Joan admits that she would love that future, but that the Doctor is needed now.
On the Family's ship, John is let aboard, fumbling about the strange interior and surrendering the watch as to stop the bombardment. When the Family opens the watch, they find it empty and realise that John has changed himself back into the Doctor. The Doctor warns the family that his early bumbling has purposely caused the ship to go into overload, and they all escape before it explodes. The Doctor then punishes the Family for their destruction, giving each of them a form of twisted immortality, such as being stuck at the event horizon of a collapsing galaxy or being trapped in every mirror in existence, when all the Doctor was trying to do was let them die out peacefully. The Doctor returns to Joan, offering her travel aboard the TARDIS but she cannot accept as she loved John but cannot come to love who the Doctor is. The Doctor gives her his Journal as she leaves. The Doctor and Martha say their goodbyes to Timothy, letting him keep the empty fob watch for himself.
A year later, as Timothy aids Hutchinson in World War I, his visions from opening the watch are able to save the two from being hit by a shell, and both survive the war. In Timothy's old age, he participates in Remembrance Sunday, and spots the Doctor and Martha from afar, both wearing artificial poppies. Timothy and the Doctor silently acknowledge each other as the service continues.

Human Nature

The Doctor and Martha narrowly escape an attack by the Family of Blood who are seeking the Doctor's Time Lord life force to prevent themselves from dying out. As the Doctor directs the TARDIS to Earth, he tells Martha that he must transform into a human for three months to escape the Family's detection while they die, and gives her a list of instructions to follow. He then uses the Chameleon Arch to transfer his Time Lord configuration to a fob watch which he entrusts Martha to guard.
After landing on earth in 1913, a year before the Great War, the Doctor adopts the persona of John Smith, a schoolteacher at Farringham School for boys, while Martha acts his maid. John's personality is nearly opposite of the Doctor's, being quiet and timid, but faint memories of the Doctor slip through, appearing as text and images he writes in his "Journal of Impossible Things". Though John carries the fob watch, the perception filter that it possesses prevents John from being curious about it. John has become infatuated with the new school nurse, Joan Redfern, and shares his journal with her; Martha remains concerned as the Doctor did not instruct her what to do should he fall in love. Timothy Latimer, a younger student at the school with extrasensory perception, discovers the fob watch and pockets it for himself, unbeknown to Martha.
Meanwhile, the Family of Blood have been able to track the Doctor to Earth, and cover their ship in an invisibility shield to keep it from being discovered. The various members of the Family seek out human victims to possess, including one of the school's prefects, one of Martha's fellow maids, a farmer, and a young girl with a balloon, allowing them to seek out the Doctor undetected. When Timothy briefly opens the watch and experiences portions of the Doctor's memories, the Family detects its presence at the school, and soon recognise Martha, trying to ply her for more information about the Doctor. Martha realises that the Family has found them and attempts to retrieve the watch in order to bring back the Doctor, but cannot find it. She attempts to talk to John to awaken the Time Lord persona, but instead causes John to become angry at her, forcing her out of his chambers as he prepares for a village dance with Joan that night. At the dance, Martha again tries to persuade John to become the Doctor by showing him elements of his past such as his sonic screwdriver, but is unaware the Family has overheard her conversation. Now aware that John is the Doctor, the Family capture both Martha and Joan. The cliffhanger ending leaves the Family asking John the question of "Maid or matron, your friend or your lover. Your choice."

42

After The Doctor adjusts Martha's phone for "Universal Roaming", they receive a distress signal from the S.S. Pentallian, a human spacecraft that is hurtling towards a nearby star, and the Doctor pilots the TARDIS towards it to help. After they materialise, the Doctor and Martha are separated from the TARDIS due to rising temperatures. They are forced to help the crew, lead by Captain McDonnell, to try to restart the engines to save the ship and themselves with only 42 minutes left before the ship will be destroyed by the nearby star. Martha teams with Riley to work their way through thirty deadlocked doors, secured via means of pop quiz questions, in order to reach the bridge controls while the Doctor helps the engineering team to repair the engines. Martha is able to call her mother, Francine, on present-day Earth in order to get the answers to some of the questions correctly, though she refuses to answer Francine's questions about the Doctor.
The Doctor learns that one of the crew, Korwin, McDonnell's husband, has been infected with something that is causing his body temperature to rise to incredible levels, and attempts to sedate him while they continue the repairs. However, Korwin manages to overcome the sedative and dons a welding helmet, proceeding to kill various crew members, and in one case, infecting another, named Ashton. As Martha and Riley continue to work through the doors, they encounter Ashton and take shelter in a nearby escape pod, which Ashton is able to launch despite Riley's attempts to stop him. As the pod falls towards the star, Martha calls her mother and apologises, but hangs up when Francine, guided by an official-looking woman listening on the conversation, probes Martha for more information on the Doctor. The Doctor learns of Martha's plight, and puts on a spacesuit to go outside the airlock and activate a magnetic pull control to recover the pod. As he returns into the ship, he looks directly into the star and becomes infected himself, while learning that the star is a living being. As the crew try to help the Doctor, McDonnell admits they drew matter from the star to use as fuel; the living being is fighting back to recover the parts it lost. Martha attempts to help the Doctor into a stasis chamber to prevent him from regenerating, while the crew continues to work towards the front of the ship. However, Korwin appears, and disables the chamber; the Doctor insists Martha to leave him and warn the crew to dump the fuel, which will allow them to escape, while the Doctor struggles to fight the star being from taking over his body.
Martha races through the ship just as the crew reach the bridge, and relays the Doctor's message. Meanwhile, McDonnell has encountered Korwin and, after apologising to him and the rest of her crew for her actions, ejects both of them out of an airlock. As the ship vents its fuel, the engines are able to be restarted and it pulls away from the star; the presence in the Doctor slowly dissipates as the ship moves away. The Doctor, Martha, and the remaining crew regroup and verify they will be safe and that the crew has send a request for more fuel so they can continue their mission. The Doctor and Martha depart in the TARDIS, the Doctor giving Martha one of the TARDIS keys. Martha places another call to her mother, and learning that it is Election Day, offers to meet her for tea. After Martha's call, the woman monitoring Francine's phone confiscates it and leaves, thanking her for her help and for her vote on behalf of Mr Saxon.

The Lazarus Experiment

The Doctor returns Martha to her flat, twelve hours relative to after she first stepped in the TARDIS. Clued in by a telephone call by Martha's mother Francine that her sister Tish is on the television, they watch a news report with a statement from the elder Professor Richard Lazarus, announcing that later that night, with one demonstration, he will "change what it means to be human". The Doctor leaves in the TARDIS, but quickly rematerialises when he recognises the impact of Lazarus' statement. They dress for the formal dinner party at Lazarus Labs, and meet up with Tish, who works for Lazarus; Francine, Martha's mother; and Leo, Martha's brother; Francine is immediately suspicious of the Doctor's interest in Martha. Their conversation is interrupted as Lazarus announced he will perform a miracle and steps into a capsule in the center of the reception room. Technicians start the machine, filling the capsule with strange energy, and the Doctor quickly steps in when he believes that the system is overloading. As the machine comes to a stop, Lazarus leaves the capsule, now a much younger man; his machine is able to manipulate the subject's DNA to make them younger. The Doctor, highly concerned of unknown side effects, is able to gain a sample of Lazarus' new DNA when Lazarus kisses Martha's hand, and, with Martha's help, discover that the DNA is unstable.
As they investigate, Lazarus returns to his office along with his partner, the elder Lady Thaw. She insists that she be the next to undergo the process so they can be young together, but he refuses as he didn't want to "waste another life with you [her]". As she threatens to have Mr. Saxon pull their funding, Lazarus begins to undergo a transformation into a scorpion-like being, and kills Lady Thaw by draining her life energy, leaving her a zombie-like corpse; after returning to his human form, Lazarus returns to the reception, while the Doctor and Martha shortly find Thaw's body, the Doctor surmising that Lazarus must drain the life energy to keep his DNA stable. The Doctor and Martha, along with Tish, quickly return to the reception area and warn everyone to escape as Lazarus transforms again. The Doctor lures Lazarus away as Martha and Tish use the sonic screwdriver to override the building's security lockdown and saving the remaining guests. Martha rejoins the Doctor and the two take shelter in Lazarus' device, the Doctor believing he will not harm his own invention. The Doctor also explains that Lazarus's transformation is the result of an evolutionary throwback locked away in dormant human genes that are now becoming dominant. Unfortunately, Lazarus manages to activate his device, but the Doctor reverses the polarity, causing the field to affect only Lazarus outside of the capsule. They emerge to find Lazarus in his human form naked and apparently dead.
As the police and medical workers arrive to take care of the wounded, Lazarus' body is taken by an ambulance. However, when the Doctor hears a nearby crash, he, Martha, and Tish race to discover the ambulance has crashed, its drivers drained of life. They find that Lazarus, alive but human, has taken shelter in Southwark Cathedral. The Doctor tries to reason with Lazarus but is unable to stop him transforming again. Martha and Tish, under the Doctor's orders, lure the creature to the top of the Cathedral's bell tower, while the Doctor manipulates the church's pipe organ to produce the maximum volume it can. The vibrations caused by the organ interfere with Lazarus' manipulated DNA, and he falls to his death to the floor below, transforming one last time to his human form.
Martha and the Doctor return to her flat, and the Doctor offers Martha on board, more than just as a passenger, which she accepts. As the TARDIS dematerialises from the flat, Martha's voice mail records Francine's warning to her daughter about the dangers of the Doctor as told to her by Mr. Saxon.

Evolution of the Daleks

After the creation of the hybrid Human-Dalek Sec, The Doctor, Martha, Frank, Laszlo, and the other human captives manage to escape when the Doctor uses his sonic screwdriver to cause a nearby radio to emit a high-pitched frequency. Daleks Jast and Caan give chase, but confer amongst themselves concern over Sec's plan. The Doctor and Martha meet up later with Tallulah, Laszlo and Frank, and make their way back to Hooverville. The Doctor warns Solomon about the Daleks and they are seeking out more human subjects, but Solomon believes he can reason with them. As the Daleks and their Pig Slaves attack, Solomon is exterminated by Dalek Caan. The Doctor, angered by Solomon's death, tells Caan to kill him as well, but Sec orders them to bring the Doctor in. Martha tries to go as well, but the Doctor makes her stay behind, giving her his psychic paper as he, along with Laszlo, leaves with the Daleks.
At the Dalek lab at the Empire State Building, the Doctor learns that Dalek Sec's plan is to continue the Dalek race by injecting humans of high intelligence with a mix of human and Dalek DNA, allowing their minds to be programmed as Daleks. However, as the task requires more energy than the human technology of 1930 can produce, Dalek Sec plans to use gamma strike from a solar flare that will occur within minutes, and forces the Doctor to help him finalise the energy system. As Sec announces that he plans to rid the intention of Dalek supremacy from these new beings, Jast and Caan believe Sec is a traitor to their race, and stage a mutiny, changing the DNA mix being fed into the humans into that of pure Dalek. The Doctor and Laszlo manage to escape during the chaos, heading for the top floors of the building. They manage to meet Martha, Tallulah, and Frank, who had used the psychic paper to gain entry from the building's human guards. After a brief reunion, they begin to search the blueprints of the building to learn how Sec planned to collect the gamma strike energy. Martha discovers the "Dalekanium" panels on the mast of the Empire State Building, and the Doctor quickly climbs up to dismount them, warning Martha of the Daleks and their Pig Slaves following them. As the Doctor struggles to remove the panels, Martha, with the help of the others, rigs several pieces of metal from the framework of the building into the elevator, acting as a long conductor of electricity when the gamma strike hits. Though Martha is successful and electrocutes the Pig Slaves in the elevator, the Doctor fails to remove the panels in time and instead grips the mast as the strike hits. The energy transfers into the human-Dalek shells and awakens the Dalek's new army.
Martha and the others recover the Doctor, and they flee to Tallulah's theater, with the human Dalek army following them in the sewers. As they are surrounded by the human Dalek army, they find that Dalek Thay and Jast have Sec in chains. As the two prepare to exterminate the Doctor, Sec tries to reason with them and then steps in the way of their blaster fire, sacrificing himself to save the Doctor. The Daleks order their army to kill the Doctor, but find that the humans are resisting; the Doctor, by exposing himself to the gamma strike, caused some of his Time Lord DNA to transfer to the human shells and give them freedom from Dalek control. The human Dalek army turn on Thay and Jast, killing them, but Dalek Caan, watching from the Empire State Building, activates a termination sequence and kills the rest of the army. The Doctor returns to the Dalek lab to face Caan, offering mercy and aid, but instead the Dalek escapes via his emergency temporal shift. As the Doctor regroups with the others, Laszlo begins to die, due to his partial transformation as a Pig Slave. The Doctor however, finds a cure to stabilise his condition, although it will not restore his human appearance. Laszlo and Tallulah are reunited, and learn from Frank that the people of Hooverville will take Laszlo in despite his looks. The Doctor and Martha finally return to Liberty Island and the Tardis, where the Doctor muses that there is to be yet another confrontation with the Daleks in their future.

Daleks in Manhattan

The Doctor and Martha, after leaving New New York, visit New York City in November 1930 (materialising the TARDIS at the base of the Statue of Liberty), before he returns Martha to her present. Stumbling across the mystery of people disappearing, they travel to the Hooverville community in Central Park and meet Solomon, the leader of the downtrodden residents, who explains more about the disappearances. When a wealthy businessman Mr Diagoras appears in Hooverville recruiting workers for sewer construction, the Doctor, Martha, Solomon, and a young man from Tennessee named Frank join up. As they explore the tunnels, the Doctor finds a mass of alien organic matter which he holds to analyse later. The group soon runs into a number of Pig Slaves and are forced to flee, though Frank is captured by the creatures.
The Doctor, Martha, and Solomon use a nearby ladder to escape and find themselves in a theater, being held at gunpoint by Tallulah, a showgirl demanding to know what happened to Laszlo, a stagehand she was dating. After the three explain their presence, the Doctor uses equipment in the theatre to create a matter analyser, while Martha helps to console Tallulah, learning that Laszlo disappeared similarly to the others a few weeks earlier. Tallulah goes on stage for her show, with Martha watching from the wings, when she spots a Pig Slave across the stage. Martha gives chase into the sewers, where she is captured by more Pig Slaves. The Doctor and Tallulah follow, but only find the sole Pig Slave Martha was chasing. Tallulah recognises him as her Laszlo, who has been incompletely transformed. They also encounter a Dalek, confirming the Doctor's analysis that shows the organic matter being from the planet Skaro. As the three follow the Dalek, they learn from Laszlo that the Daleks either transform those humans with low intelligence into the Pig Slaves, or take those of high intelligence aside for a "final experiment".
They find themselves under the incomplete Empire State Building, and the Doctor and Laszlo sneak inside to locate Martha. When the Doctor and Laszlo join both Martha and Frank with the rest of the high intelligence captives, they find that the Cult of Skaro are working on experiments to merge the Dalek and Human races so that the Dalek race can continue, assisted by Mr Diagoras during the construction of the Empire State Building. Dalek Sec plans to sacrifice himself to prove to the others that their evolution is possible. Dalek Sec, using energy collected by panels of "Dalekanium" attached to the mast of the Empire State Building, fuses himself to the body of Mr Diagoras, becoming a hybrid creature, and proclaiming himself as a "Human Dalek" and the future of the Dalek race.

Gridlock

The Doctor takes Martha with his TARDIS to the year five billion and fifty three in New New York on the planet New Earth, a place to which he had previously taken Rose Tyler. They end up in an alleyway where street traders are selling mood patches to help people deal with "The Motorway", but as they are investigating this, Martha is kidnapped at gun point and drugged by a young couple, Milo and Cheen. Once in their vehicle, they explain that Cheen is pregnant and that they needed three adult passengers to qualify for the high-occupancy vehicle lane, the "Fast Lane", and that they will drop Martha off when they reach their destination 10 miles (16 km) away in six years. Cheen also mentions rumours about something living down in the fast lane, saying that cars that go down there vanish, never to be seen again.
The Doctor chases after Martha's kidnappers and arrives at the (entirely enclosed) Motorway to find thousands of hover vans stuck in a tri-dimensional gridlock. The fumes in the air begin to affect the Doctor, but he is invited into the hover van of the cat person Thomas Kincade Brannigan and his human wife Valerie, who have a litter of kittens. The Doctor learns that the couple, along with all the other traffic on the road, has only travelled a short distance in several years, their vans having become their homes. Brannigan helps the Doctor to locate the vehicle containing his companion, heading towards the Fast Lane. As the Doctor tries to call the Police but gets put on hold and Brannigan refuses to put his family in danger, the Doctor decides to try and reach Martha himself and begins to jump down from lane to lane, breaking in and out of vans with his sonic screwdriver. Shortly after the Doctor leaves Brannigan's van, Novice Hame, who has been sent by the Face of Boe to locate the Doctor, enters Brannigan's van, chasing after him.
Martha, Milo, and Cheen drive into the Fast Lane, and begin to hear strange noises all around, and a nearby driver warns them to escape into the slow lanes before being eaten by the creatures that live in the fast lane, but Milo refuses. The Doctor, finding himself in a van just above the Fast Lane, looks out the bottom and discovers that the floor of the Motorway is filled with Macra, monstrous crab-like alien beings that once ruled an empire but now have devolved into feral, non-sentient beasts, who attempt to capture and eat those that fly in the Fast Lane. As the Doctor watches, Milo's van is nearly caught by one Macra's huge claw, but Martha realises that the beings are attracted by the light and motion generated by the van, and has Milo cut the power. This saves them from the beasts but leaves them with only a few minutes of breathable air in the van.
Novice Hame finally catches up with the Doctor and teleports him away forcefully to the Senate where the Face of Boe is waiting. Hame explains that a "Bliss" drug created by the pharmacists mutated into a virus that became airborne and wiped out the entire surface population, and only those in the Motorway were spared due to her actions to seal it off, keeping the travellers in constant traffic to avoid telling them the real problem. The Face of Boe has wired himself to the system to keep the Motorway operational. The Doctor determines that whatever danger that "Bliss" may have caused before has long passed, and works with Hame to try to power up the systems to unseal the Motorway but there is not enough energy left. The Face of Boe sacrifices his life energy to the system, allowing the ceiling of the Motorway to open, and the Doctor broadcasts a call for all drivers to escape that way and for Martha to come find him.
When Martha does so, the Doctor and Novice Hame are tending over the Face of Boe who is finally close to death; the glass container that encased it had shattered. The Doctor tries to encourage the Face of Boe to live, as both the Doctor and the Face of Boe are the last of their respective kinds, but with its dying breath it whispers the secret it promised to tell the Doctor before: "You are not alone". As the Doctor and Martha leave Hame to mourn, the Doctor does not try to postulate the meaning of those words, but explains to Martha that he is indeed the last Time Lord, and tells her all about Gallifrey as they return to the TARDIS.

The Shakespeare Code

A young woman is serenaded from her balcony by a lute-playing suitor. She bids him enter the house, but to his shock he finds it full of witching artefacts. The woman, Lilith, kisses him, and he finds her transformed into a wrinkled hag. She introduces her two "mothers", Doomfinger and Bloodtide, who appear, cackling; they lunge at the screaming youth, apparently devouring him.
Meanwhile, the TARDIS lands in Elizabethan London. Martha questions whether it is safe to walk around, citing such time travel concepts as the Grandfather paradox and a reference to the Ray Bradbury short story "A Sound of Thunder"; and also worrying about her safety as a black woman in a time when slavery still exists. The Doctor tells her not to worry. He declares that they have arrived in London in about 1599 and takes her to a performance at the Globe Theatre. At the end of the play, Love's Labour's Lost, Shakespeare announces that there will soon be a sequel called Love's Labour's Won. Lilith, using a poppet, influences Shakespeare to declare that the new play will premiere the following evening. Martha asks why she has never heard of Love's Labour's Won. The Doctor knows of the lost play and, decides to find out more about why it was never published — extending Martha's "one trip".
The two go to The Elephant, the inn where William Shakespeare is staying. They chat with the playwright, who intends to finish writing the final scene of Love Labour's Won that night. An instantly beguiled Shakespeare ("Hey, nonny nonny!") tries to woo Martha, describing her as "a queen of Afric" or a "blackamoor lady", which she finds slightly offensive. The Doctor claims she comes from "Freedonia" to explain her strange clothing and modern attitudes. Shakespeare sees past the Doctor's psychic paper, which the Doctor cites as proof of the man's genius.
Lynley, Master of the Revels, demands to see the script before he allows the play to proceed. When Shakespeare offers to show him the finished script in the morning, the official leaves proclaiming that he will ensure the play will never be performed. The trio of "witches" view the scene remotely by looking into a cauldron. Lilith, who works at the inn, secretly takes some of Lynley's hair and makes another poppet, which she plunges into a bucket of water. The Doctor, Martha, and Shakespeare hear a commotion in the street and run out, where they witness Lynley vomiting water. Lilith stabs the doll in the chest, and Lynley collapses, dead. The Doctor calmly announces that Lynley has died of an imbalance of the humours, and privately tells Martha that any other explanation would lead to panic about witchcraft. When Martha asks what did kill Lynley, the Doctor responds, "Witchcraft."
Martha and the Doctor stay overnight at the inn. The Doctor gives a disgruntled Martha mixed signals by casually sharing a bed with her, only to then openly bemoan the lack of Rose's insight. Meanwhile, Lilith entrances Shakespeare and, using a marionette, compels him to write a strange concluding paragraph to Love's Labour's Won. She is discovered by the landlady (also the Bard's lover), whom she frightens to death. On hearing another scream, the Doctor runs in and finds the body. Through the window, Martha sees a witch fly away on a broomstick.
In the morning the Doctor, Martha and Shakespeare proceed to the Globe Theatre, where the Doctor asks why the theatre has 14 sides. Shakespeare replies that the architect thought it would make sound carry well and mentions that he eventually went mad and talked of witches. The three then visit the architect, Peter Streete, in Bedlam Asylum. The Doctor helps Streete to emerge from his catatonia for long enough to reveal that the witches dictated the Globe's design to him. He also tells the Doctor that the witches were based in All Hallows Street.
The witches observe this interview through their cauldron. Doomfinger teleports to the cell and kills Peter with a touch. She threatens the other three but the Doctor works out who the witches really are. He names the creature as a Carrionite, which causes her to disappear. The Doctor explains that the Carrionites produce their magic through an ancient science based on the power of words.
Back at the Elephant, the Doctor deduces that the Carrionites intend to use the words of a genius — Shakespeare — to break their species out of eternal imprisonment when Love's Labours Won is performed. The Doctor tells Shakespeare to stop the play whilst he and Martha go to All Hallows Street to thwart the witches. The Doctor explains to Martha that if they don't stop the Carrionites, she and the rest of the human race will fade, much the same as Marty McFly. Shakespeare bursts on to the Globe's stage to make the announcement, but two of the Carrionites use one of their dolls to render him unconscious. The actors carry the playwright off stage and the performance proceeds.
The Doctor and Martha reach All Hallows Street and confront Lilith, who is expecting them. She confirms the Doctor's suspicions: the three Carrionites hope to gain entry for the rest of their species, eliminate the humans, begin a new empire on Earth and spread out from there. Martha, mimicking the Doctor's actions at Bedlam; tries to neutralise her by speaking the name Carrionite, but Lilith mocks her, since naming only works once. Instead, she names Martha Jones, rendering her unconscious.
Lilith tries to do the same to the Doctor, but it fails to affect him, as she is unable to discover his real name. She attempts to weaken him by naming "Rose", but he assures her that that name keeps him fighting. Lilith then feigns an attempt at seduction, which brings her close enough to the Doctor to steal a lock of his hair. Taking flight through the window, she attaches the hair to a doll — which the Doctor explains is essentially a DNA replication module — and stabs it in the heart, whereupon the Doctor collapses. Assuming that he is dead, Lilith flies to the Globe. Martha wakes, and helps the Doctor restart his left heart before the duo race to the Globe.
The actors have already spoken the last lines of the play, a series of directions and instructions that have opened a portal allowing the Carrionites back into the universe. The Doctor tells Shakespeare that only he can find the words to close the portal. Shakespeare improvises a short rhyming stanza but is stuck for a final word. Martha comes up with Expelliarmus which is shouted at the Carrionites (as shown in the picture). The Carrionites — together with all the extant copies of Love's Labour's Won — hence, are sucked back through the closing portal. Martha, Shakespeare and the actors from the play are left to take the applause of the audience who believe it all to be special effects. The Doctor meanwhile finds the three witches trapped, screaming in their own crystal ball and appropriates it for safe keeping in a dark attic of the TARDIS.
In the morning, Shakespeare flirts once more with Martha and with the Doctor. He reveals his deduction that the Doctor is not of the Earth and that Martha is from the future, once again proving his genius. For his "Dark Lady", he produces the sonnet, "Shall I compare thee to a summer's day?" in her honour, but is interrupted when two of his actors burst in, heralding the arrival of the Queen. Queen Elizabeth enters, recognises the Doctor as her "sworn enemy" and declares, "Off with his head!" The Doctor is surprised at her outburst, since he says he has not yet met the Queen, but comments that he is looking forward to finding out what he will do to offend her. He and Martha flee to the TARDIS, slamming the door just as an arrow embeds itself in the TARDIS's exterior before dematerialisation.

Smith and Jones

Martha Jones is a particularly astute medical student. On her way into work at a London hospital, she bumps into a strange man (the Doctor) who pauses in front of her and removes his tie, saying, "Like so, see?" When she arrives at work, she again meets the Doctor, who is lying in bed posing as a patient under the name John Smith. He is unaware of seeing Martha earlier in the morning.
A brutal mercenary police force, the rhinoceros-like Judoon, who have no jurisdiction on Earth, transport the hospital to the Moon using a "H2O Scoop" in order to apprehend and execute Florence Finnegan, a shapeshifting, bloodsucking Plasmavore with the ability to appear as whatever species whose blood she consumes. As soon as the hospital is in position, the cylindrical Judoon ships land and the troopers march into the building (due to their bodily shape and heavy footwear, their motion is referred to throughout the script as "yomping"). The Judoon begin scanning everyone in the hospital, cataloguing the humans whilst attempting to find the non-human criminal. Finnegan attempts to evade capture by sucking the blood of humans. Her first victim is Mr Stoker, the head doctor, and consequently she registers as a human when scanned by Judoons. The Doctor is identified as "non-human" and thus is thought to be the fugitive by the Judoon, forcing him and Martha, with whom he teamed up shortly after arriving on the Moon, to flee.
The Doctor and Martha discover Stoker's body drained of blood which confirms the Doctor's suspicion that a Plasmavore is in the hospital, this in turn explaining the Doctor's presence there to the audience. The Doctor kisses Martha, performing a "genetic transfer" which provides her with traces of contact with a non-human. He leaves her behind to be fully scanned by Judoon, providing him with more time as he goes in pursuit of the Plasmavore. Thinking the Doctor is human, Finnegan sucks his blood causing him to collapse unconscious, presumed dead. Judoons arrive and confirm the non-human is deceased. Martha enters, realises that Finnegan has absorbed non-human blood, grabs a Judoon's scanner and identifies Finnegan as non-human. Confirming Finnegan is a Plasmavore, the Judoon execute her for the murder of the child princess of Padrivole Regency Nine.
Before expiring, Finnegan modified an MRI scanner to make it destroy all life on the Moon and on the half of Earth facing the Moon except herself, thus allowing her to use the Judoon ships to escape. Their job done, the Judoon evacuate. Martha uses CPR on the Doctor's two hearts and manages to revive him, and he turns off the scanner. Oxygen levels are low and the occupants of the hospital are near death but, as they depart, the Judoon return the hospital safely to Earth.
Martha attends her brother's birthday party, but it breaks down into a family row. She notices the Doctor outside and follows him. He goes to the TARDIS and invites Martha to go on a trip with him as a reward for her help. Martha hesitates until the Doctor says he can travel in time as well, and proves it by travelling back to the previous morning and taking off his tie in front of Martha (later explaining, "Crossing into established events is strictly forbidden — except for cheap tricks"). After this demonstration, Martha steps into the TARDIS (noting that it's bigger on the inside). The Doctor refers to Rose Tyler and emphasises that Martha is not replacing her but is only going to get one trip as he prefers to travel alone.