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In both the original run and since the 2005 revival, the long-running British science fiction television programme Doctor Who has featured a number of story arcs. A story arc is an extended story which takes place over a large number of episodes or serials, characterised by a gradual unfolding of plot points and introduction of narrative devices which come together in the arc's climax and dénouement. While character arcs exist over the course of many stories, they do not necessarily take the shape of an expanded story arc.
References to these arcs have since been made in both Doctor Who and its spin-offs such as Torchwood. Early seasons would feature story arcs that made up extended serials such as The Trial of a Time Lord but also loose umbrella titles such as The Key to Time. The new series has continued this trend with the introduction of "arc words" that are recognisable to the larger viewing audience such as "Bad Wolf", "Torchwood" and "Mr Saxon", which also constitute the story arcs for individual seasons.
The classic series sporadically featured loose story arcs at several times in the series, often spanning half of a season or a full season. Several story arcs were later released on DVD as boxsets; for example, The Key to Time
Season 8 of Doctor Who involved the first appearance of the Doctor's arch enemy, the Master, portrayed then by Roger Delgado. Every story in the season involved the Master. At the very beginning, the Doctor is warned by a Time Lord that the Master, a convicted criminal and enemy of the Doctor's, has escaped from Gallifrey and may come to Earth seeking revenge. This proves to be the case. During this first story, the Doctor sabotages the Master's TARDIS and so traps the Master on Earth in the 20th century. The Master later retrieves a missing component and escapes – only to return subsequently as a prisoner of Axos. He is next encountered in the future on an alien world and finally returns to Earth; in both of these last two adventures, his intention is to subvert an ancient power source, having previously stolen secret files on such things from the Time Lords. At the very end of the season (in The Dæmons), UNIT finally captures the Master and takes him into custody.
The majority of season 12 features an ongoing plot involving a space station in orbit around Earth- which is visited in two different time periods- the fate of Earth in this time period, and a temporary detour on a mission for the Time Lords, culminating in the TARDIS crew returning to the space station in the past and being reunited with the TARDIS in time to receive an emergency call from UNIT, leading into the season 13 opener.
Season 13 saw the departure of Harry Sullivan, returning to just the Doctor and Sarah Jane travelling in the TARDIS. It also saw one of the three final appearances of the Brigadier for the rest of the series. For most of the season, an arc of the TARDIS continuously failing to land at the correct time and place UNIT HQ was used. They usually ended up in the right place, wrong time; or wrong place, right time.
This arc helped gradually phase UNIT out of Doctor Who; due to his exile in seasons 7 – 9, the Doctor's adventures had mostly been tied to present day earth with few trips to different times and planets, since he worked as UNIT's scientific advisor. Due to the Doctor never managing to land the TARDIS back at his laboratory at UNIT HQ, audiences were allowed to gradually get used to the Doctor resuming his uninterrupted travels through time and space.
The Key to Time is the umbrella title that links all six serials of Season 16 of Doctor Who. The arc was originally conceived of by producer Graham Williams, who had proposed it as part of his application for the producer's job in 1976. The name refers to the powerful artifact whose segments the Doctor, Romana and K-9 are searching for during the season.
A figure calling himself the White Guardian commissions the Doctor and K9, assisted by a new companion, the Time Lady Romana, to find the six segments of the Key to Time, a cosmic artifact resembling a perfect cube that maintains the equilibrium of the universe. Since it is too powerful for any single being to possess, it has been split into six different segments and scattered across space and time, disguised by the raw elemental power within them into any shape or size. However, since the forces balancing the universe are so upset, the White Guardian needs to recover the segments of the Key to stop the universe so that he can restore the balance. The White Guardian also warns the Doctor of the Black Guardian who also wishes to obtain the Key To Time for his own purposes.
The first segment is disguised as a chunk of mineral rock (called Jethryk) on the planet Ribos. The second is the planet Calufrax, shrunk to miniature size by the space-hopping pirate planet Zanak. The third is the Great Seal of Diplos, which has been stolen by a criminal of that planet. The fourth is part of a statue on the planet Tara. The fifth has been consumed by the squid Kroll, causing it to turn into a gigantic monster. The final segment is actually a living person, Princess Astra.
In the final episode, the Black Guardian, disguised as the White Guardian, attempts to take the Key from the Doctor. However, the Doctor sees through the figure's charade and orders the segments of The Key to Time to once again become scattered across all of time and space, bar the sixth, which he reinstates as Princess Astra. Afterward, the Doctor decides to install a device called a randomiser into the TARDIS navigation system for a period of time to make his following voyages unpredictable to evade the Black Guardian.
The entire Key To Time season encompasses 26 episodes, with a complete running time for all six serials in the arc at 633 minutes.
The Black Guardian returns in the 1983 three serial arc, The Black Guardian Trilogy involving the Fifth Doctor and Vislor Turlough.
The Key to Time is available on DVD in North America and was released on region 2 (Europe) DVD on 24 September 2007.
Key 2 Time is a series of CD audio plays released by Big Finish Productions. Over the course of three stories, the Fifth Doctor must hunt down the redistributed segments of the Key, which are decaying the dimensions around them. The Doctor soon discovers the decay is a direct result of his actions in the first search for the Key, his attempt to assemble the Key using a makeshift sixth segment disrupting the balance between the segments and causing them to decay. The story ends with the Key being reassembled and the Doctor subsequently destroying the Key in the Chaos Pool where it was first made, undoing the damage it has caused and preventing anything from ever using the Key again. The three stories are The Judgement of Isskar, The Destroyer of Delights and The Chaos Pool.
All serials of season 18 are linked together by the central theme of entropy. Within the season, the stories Full Circle, State of Decay and Warriors' Gate form the sub-arc known as The E-Space Trilogy. The trilogy saw the TARDIS accidentally pass through a Charged Vacuum Emboitment (CVE) from its normal universe, N-Space, into a smaller one called E-Space. The trilogy served to introduce Adric as a companion in the first story Full Circle and marked the departure of companions Romana and K-9 Mark II in the final story Warriors' Gate. The season culminated in Logopolis where we learn that the CVEs were created by the Logopolitans to combat an Entropy field that ends up growing out of control due to interference by the Master, destroying Logopolis and threatening to destroy the entire universe.
Overlapping the entropy arc are these three stories which cover the regeneration into Peter Davison's Fifth Doctor, chronicles the Master as he attempts to procure a new body, and return to his old patterns of trying to conquer the universe and defeat the Doctor. The trilogy was also used to introduce Nyssa of Traken and Tegan Jovanka as the Doctor's new companions. They were released on DVD in 2007 under the title New Beginnings.
During these three stories in season twenty, the Black Guardian tries to have the Doctor assassinated for denying him the Key to Time. To this end, he employs the mysterious extraterrestrial English boys' school student Vislor Turlough who eventually joins the TARDIS crew and companion Nyssa departs.
The Trial of a Time Lord is the title of the fourteen-part serial that encompasses the entirety of Season 23. In the serial, the Sixth Doctor stands accused of transgressing the First Law of Time, with adventures from his past, present, and future examined and used as evidence of guilt or innocence. As the case unfolds, it becomes clear that the Doctor is the victim of an elaborate conspiracy, with his memories of recent events blurred due to the circumstances of him being removed from time, the evidence against him being either doctored or missing crucial information, and his prosecutor, the Valeyard, having an undetermined final objective. The story concludes with the Doctor defeating the Valeyard- identified as the manifestation of his own evil nature- and being cleared of all charges against him.
Fenric is a loose story arc covering Ace's time in the TARDIS with the Doctor from the end of Season 24 to near the end of Season 26. It involved a malevolent entity known as Fenric, that was beaten by the Doctor in a game of chess some unknown time in the past and banished to a different dimension. Since then, he had been setting up a series of events leading to his return, and those that are influenced by these are considered the "wolves of Fenric". One such example is Ace; Fenric created the time storm that brought Ace to the planet Svartos so that she will become the Doctor's companion, and later uses her as a pawn not only to assure that Ace's own timestream is preserved but as to defeat the Doctor (The Curse of Fenric). Fenric was also responsible for giving Lady Peinforte, an evil 17th-century sorceress in Silver Nemesis, the power to travel through time. This was also part of the initial story setup for the Cartmel Masterplan which never came to full realization, though the concept was later explored in the Virgin New Adventures spinoff books.
In the revived series of Doctor Who, story arcs span an entire series. Under Russell T Davies, these arcs involved a repeated phrase that generally went unnoticed by the characters, only receiving any actual story-based attention when they were explained in the finale. In contrast, Steven Moffat's arcs have been evolving storylines woven through individual episode plots, with entire episodes dedicated to more information given to the characters.
The Time War has been a subject developed since the revival, first explained in the 2005 series to have been between the Time Lords and the Daleks. The Doctor has discussed this war, claiming that both sides had been wiped out through space and time by his own hand. However, the Doctor finds himself facing surviving Daleks throughout the duration of his Ninth and Tenth Incarnations with the latter encountering the Master and Davros. In the 2009 special, The End of Time, the Doctor's reasons for ending the Time War are revealed at the end of Davies's duration as series writer; the Time Lords, led by Rassilon, intended to allow the universe to be destroyed while they survived by ascending to a level of pure consciousness, the Doctor refusing to allow the universe to die just to save his people.
When Steven Moffat replaced Davies as Executive Producer of Doctor Who in 2009, he invented the War Doctor to conclude the Time War story arc for the fiftieth anniversary of the series with a short episode, "Night of the Doctor", serving to formally introduce the incarnation to be between the Eighth Doctor and the Ninth Doctor, his existence 'ignored' by his future selves as he deliberately forsook the title 'Doctor' in favour of being the warrior he believed the universe needed instead. In "The Day of the Doctor", on the last day of the Time War, it is revealed that the War Doctor was ready to use the Moment, a sentient weapon of mass destruction, to destroy Gallifrey and the Dalek fleet, but its consciousness challenges him over the morality of his actions and opens time fissures in order for him to meet his future regenerations (the Tenth and Eleventh Doctors) before he can activate it. The two future incarnations listen to the War Doctor's plight, and, both lacking memories of this time, agree that it is for the best and offer to help shoulder the burden. However, at the last moment and at the insistence of companion Clara Oswald, they come up with a different plan – to freeze Gallifrey in a fixed moment of time. This would cause the planet to disappear and the attacking Dalek fleet to destroy themselves; to the rest of the universe, it would still appear as if the two sides had wiped each other out. The three Doctors bring all their other incarnations – including their future thirteenth incarnation – and their respective TARDISes to manipulate Gallifrey into stasis (as the calculations necessary require centuries), and with the consent of the now-desperate Time Lords they are successful. As the Doctors say their goodbyes, the War Doctor and the Tenth Doctor realize they will forget these events to avoid a time paradox; the War Doctor will continue to believe that he attempted to destroy Gallifrey rather than save it, but accepts this as necessary. The Eleventh Doctor, now aware that Gallifrey still exists, makes it his mission to bring the planet back out of stasis.
The phrase "Bad Wolf" first appeared in episode 1 of the 2005 series, when the Nestene Consciousness uttered it to The Doctor, redubbed more clearly for the DVD releases. In episode 2, the Moxx of Balhoon spoke the phrase, "Indubitably, this is the Bad Wolf scenario", and then the phrase appeared in every story of that series thereafter. It also occasionally appeared in the 2006 to 2008 series and even in 2013 as the show celebrated its 50th anniversary, as well as in online and print spin-off media; in the latter, it often constitutes an in-joke or a continuity nod. It was eventually revealed that "Bad Wolf" was actually Rose Tyler, who had gained godlike powers after absorbing the energy of the time vortex at the heart of the TARDIS, while attempting to get back to Satellite 5 to help The Doctor defeat the Daleks in "The Parting of the Ways", which granted her omnipotent reality warping abilities.
When she arrived, Rose destroyed the entire Dalek fleet, including the Dalek Emperor, and brought Captain Jack Harkness, who had been killed by the Daleks, back to life; he became effectively immortal as a result. She also took the words "Bad Wolf" from the sign in Satellite 5 and spread them through all space and time as clues for her past self to return to Satellite 5 and save the Doctor (i.e., to do what she had just done).
The Doctor then had to extract the time vortex from Rose before it killed her. He did this by kissing her and absorbing the energy himself, which saved her life but caused all the cells in his body to start decomposing, so that he had to regenerate.
I am the Bad Wolf. I create myself. I take the words. I scatter them ... in time, and space. A message to lead myself here.
— Rose Tyler, in "The Parting of the Ways".
The 2006 series featured "Torchwood" as its arc word, an anagram of "Doctor Who" that was used as the codename for the new series of Doctor Who while filming its first few episodes and on the 'rushes' tapes to ensure they were not intercepted.
The word first appeared in Doctor Who in the 2005 series episode "Bad Wolf", as an answer in the game show, The Weakest Link. The actual "Torchwood" arc of Doctor Who spanned from "The Christmas Invasion" to "Doomsday". The word was seeded throughout the 2006 series as a means for the BBC to introduce the basis for a spin-off series, Torchwood, set in modern-day Cardiff and involving a mysterious organisation which investigates alien activities and crime. The series features John Barrowman as former companion Jack Harkness and premiered in October 2006. References to Torchwood have also since reappeared in Doctor Who. The Doctor and Rose repeatedly encountered mentions of "Torchwood" throughout the series until the episodes "Army of Ghosts" and "Doomsday", which included Torchwood as an integral part of the plot. Here the Doctor meets the organisation, and learns they have been monitoring him (his Tenth incarnation) since his encounter with Queen Victoria in "Tooth and Claw". As a conclusion of the story arc, the Torchwood Institute's London branch was destroyed. In addition to episodes of the 2006 series, the organisation was given a similar treatment to "Bad Wolf" in spin-off material such as web literature, webcasts and novels.
The name "Mr Saxon" has appeared several times, beginning with a newspaper headline in "Love & Monsters" in Series 2 (2006), and continuing with a mention of him in dialogue in "The Runaway Bride" (2006), where it was established as the new arc word for Series 3 (2007). In "Smith and Jones", the first episode of the third series, his name is mentioned in a radio broadcast stating; "It all just proves Mr. Saxon right, we're not alone in the universe." A "Vote Saxon" poster is seen in the background when Martha Jones is invited into the TARDIS by the Doctor; an identical poster had previously been seen in the Torchwood episode "Captain Jack Harkness". The arc was more thoroughly explained in "The Sound of Drums" (2007), which connected the rise of the mysterious Mr Saxon as a new Prime Minister to an old enemy of the Doctor's, as well as the fall of Harriet Jones (Penelope Wilton) from office at the Doctor's own hands after she ordered Torchwood to shoot down the Sycorax spaceship during "The Christmas Invasion".
In "Utopia", when the resurrected Master (John Simm) attempted to steal the TARDIS, the Doctor used his sonic screwdriver to lock the TARDIS to no more than 18 months prior to its last location, which was April 2008, and therefore October 2006. Arriving in Britain during the power vacuum left by Harriet Jones' departure, the Master created an alias for himself as "Mr Harold Saxon" ("Mister Saxon" is an anagram for "Master No. Six", "No." being short for "Number"), and quickly rose to prominence as Secretary of State for Defence; he redesigned the cabinet rooms destroyed during "World War Three", established the "Archangel network" of satellites, and commissioned the UNIT aircraft carrier Valiant. Using the Archangel network, Saxon sent subliminal messages encoded in the sound of drums to cause the British people to trust him and ensure his election as Prime Minister. The satellite signal also counteracted the Doctor's telepathic ability to sense the presence of another Time Lord on Earth.
The Master began setting traps for the Doctor through his companion Martha (Freema Agyeman) and her family. He funded Professor Lazarus's genetic rejuvenation experiments in "The Lazarus Experiment", and ensured that Lazarus hired Martha's sister Tish (Gugu Mbatha-Raw) to lure the Doctor. Using the events of "The Lazarus Experiment" at LazLabs as a catalyst, he ensured Martha's mother Francine's distrust of the Doctor, and manipulated her to trace Martha's phone calls on her superphone. When the Doctor, Martha and Jack (John Barrowman) return to Earth in 2008, the Master had established his identity as Mr Saxon, and married Lucy Saxon (Alexandra Moen). He ruled Earth for a year, but was eventually defeated when the world's remaining population – united by Martha's stories about the Doctor – psychically connected to the Doctor, enabling him to rejuvenate himself and overpower the Master.
Russell T Davies hinted in Doctor Who Magazine that the next arc word for Doctor Who was something spoken by The Master in the final two episodes of Series 3—"The Sound of Drums" and "Last of the Time Lords". He has since stated that there is no specific arc word, but each episode of Series 4 would have an element of the arc theme, which would carry through to the finale.
Four takes a somewhat different approach to the previous series. Russell T Davies says: "You've got to watch and listen closely. It's been seeded for a long time, with small but vital references going all the way back to series one. And remember the Master, in 'Last of the Time Lords', mentioning the Medusa Cascade? Oh, that's going to come back to haunt us..."—Doctor Who Magazine No. 394 [clarification needed]
Series 4 is seeded with allusions to different planets disappearing. In "Partners in Crime", Miss Foster reveals that the Adipose breeding planet (Adipose 3) was "lost". Donna also makes a passing reference to all of the bees on Earth disappearing. In "The Fires of Pompeii" the Pyroviles tell The Doctor that their home planet of Pyrovilia was "lost" ages ago. In the episode "Midnight", Dee Dee tells The Doctor that she wrote a paper on the lost moon of Poosh. The season's finale, the two-part story "The Stolen Earth" and "Journey's End", sees the climax of many references and events made over the course of the entire revived series. The disappearing bees are explained as bees being alien in origin and leaving the Earth in anticipation of its "theft" from space by Davros (Julian Bleach). The Doctor later reveals that the 27 missing planets (including the three referenced earlier) were a second out of sync with normal time (as were components of the ATMOS devices from the episode "The Sontaran Stratagem") and hidden in the Medusa Cascade, an area of space previously mentioned by the Master and the Doctor, and visited by the latter when he was – in his own words, "just a kid" – ninety years old.
It was noted by Ood Sigma in "Planet of the Ood" (2008) that the Doctor's "song" would be ending soon. In reference to the Doctor's encounter with a man he believes to be his future regeneration, in "The Next Doctor", Russell T Davies commented to the Radio Times: "The Doctor finds himself staring at that inevitable day when his tenth incarnation must die." For the 2009–10 specials, beginning with "Planet of the Dead", a prophetic character tells the Doctor, "It is returning. It is returning through the dark, and then Doctor... oh but then... he will knock four times." Subsequently, in "The Wedding of Sarah Jane Smith" (a crossover with The Sarah Jane Adventures), the Trickster mentions that "the Gate" is waiting for the Doctor that also foreshadows his death. In "The Waters of Mars", the Doctor contemplates the four knocks; he tries to save the life of Adelaide Brooke (Lindsay Duncan), whose death is a fixed point in time, and tries to prove to himself that he is above the laws of time. Ood Sigma later appears to the Doctor, who takes it as a sign of his impending death. The Doctor defiantly takes part in a number of adventures, one being his marriage to Queen Elizabeth I, to delay the eventuality.
In The End of Time, after learning that the revived Master is key to the return of something else, realizing his association with the Noble family has not ended yet, the Doctor finds himself seeing Wilfred Mott (Bernard Cribbins) again. The Doctor confides in Wilf that he had grown attached to the individual identity of his present incarnation, fearing a literal death while expressing his displeasure towards regeneration as he would cease being himself with "new man" taking over where he left off. Eventually, the Doctor learns that the Master was a pawn to free Gallifrey from the Time Lock, the deed made in Rassilon's design as part of a plan to destroy time itself while Time Lords ascend victorious beyond time and space as beings of consciousness. The Doctor thwarts Rassilon's plan, and believed he would survive until hearing four hesitant knocks—Wilfred is trapped within a sealed radiation chamber that powered the Eternity Gate. Eventually coming to terms that only way to save the old man is by sacrificing himself, the Doctor switches places with Wilf while absorbing the flooding radiation. Holding off his regeneration for as long as possible, the Doctor visits the Companions he had throughout his incarnation's time before finally regenerating into the Eleventh Doctor.
In the first episode of Series 5, the newly regenerated Eleventh Doctor (Matt Smith) meets young Amelia Pond (Caitlin Blackwood) who shows him a crack in her bedroom wall that he recognises as a crack in "the skin of the universe". This crack affected Amy's life, erasing her parents from history and let Prisoner Zero enter Leadworth. As the Doctor begins his journey with an adult Amy Pond (Karen Gillan), joined by her fiancé Rory (Arthur Darvill), he is unaware of similar-shaped cracks that appear in various moments in time, such as in the hull of Starship UK in "The Beast Below", on a wall in the Cabinet War Rooms in "Victory of the Daleks" and in a kitchen in "The Lodger". The nature of the cracks is revealed in "Flesh and Stone", when the Doctor discovers that the crack is a result of a time explosion on 26 June 2010, the day of Amy's wedding to Rory and the danger it posed. The Doctor also learns that the cracks are also the result of the TARDIS exploding.
In "The Pandorica Opens", River Song (Alex Kingston) recovers a work of Vincent van Gogh (Tony Curran) showing the destruction of the TARDIS; the Doctor connects the painting with the Pandorica. The Pandorica is revealed as a trap for the Doctor created by his greatest foes from elements of Amy's childhood imagination, designed to lock the Doctor away and prevent the timestream damage that they believe the Doctor will cause, even though the Doctor warns that the time explosion will be caused by the exploding TARDIS. When, in "The Big Bang", the TARDIS explodes with River inside, a sinister hissing voice is heard declaring 'silence will fall'. The explosion destroys every star in the universe and all goes dark, except for the Earth, which appears to have a sun keeping it alive. This light source is revealed to be the exploding TARDIS, having put itself into a time loop at the moment of its own destruction to save River Song. After exploiting a time paradox to escape the Pandorica, the Doctor uses the remaining atoms of the original universe inside the Pandorica to restore the universe to normal—comparing it to cloning a body from a single cell—and closes the cracks, albeit with him sealed away from the universe behind them. He is returned to the universe after Amy, during her wedding, recalls the last words the Doctor said to her as a child. After returning to the universe, the Doctor remains concerned at what caused the TARDIS to explode in the first place. It would be during the events of "The Time of the Doctor", when he finds one crack left unclosed, that the Doctor discovers who was behind the explosion.
While previous series have used an "arc word" to tie episodes together, series 6 used a more serialised plot, encompassing a larger story over the entire run. Series 6 continues to explore the significance of the phrase "silence will fall", left unresolved from series 5. Series 6 also focuses upon the true identity of River Song, who was introduced in series 4 as future ally of the Doctor in his Eleventh Doctor incarnation.
Invited by the Doctor to Utah alongside River Song, Amy and Rory witness his death on 22 April 2011 on the shores of Lake Silencio by an unknown figure in a spacesuit. The three later encounter a two-hundred years-younger version of the Doctor, and vow not to tell him about this death while going to America 1969 on the future Doctor's behalf. Their adventure and initial encounter with the Silence has Amy encounter the mysterious astronaut, revealed to be a little girl. Meanwhile, the Doctor discovers that Amy is pregnant and, while investigating how she can be both with child and without, learns she has been kidnapped by Madame Kovarian and Silence. But the Doctor learns that Kovarian is actually after Amy's newborn child Melody, who possesses Time Lord-like DNA due to being conceived aboard the TARDIS during Amy and Rory's wedding night, to condition into an assassin to kill the Doctor. Though the Doctor learns he failed to rescue Melody, he does learn that she will one day become River Song.
Having escaped the Silence in "Day of the Moon", Melody regenerated into Amy and Rory's common childhood friend Mels and kept a low profile until she forces the Doctor to take them to the past so she can kill Adolf Hitler. But Mels ends up regenerating into the woman they recognise as River. River poisons the Doctor, but Amy, Rory, and the Teselecta convince her to break her conditioning and use her remaining regenerations to save the Doctor. The Doctor takes the unconscious River to the far future and leaves her there to heal. When she recovers, she becomes a student of archeology to track down the Doctor, but is later recaptured by Kovarian and the Silence to play her role in the Doctor's death at Lake Silencio. The Doctor, having learned of his death being a fixed point, leaves Amy and Rory on Earth for their own safety while he traveled the universe for two hundred years. Learning that the Silence are a religious order bent on keeping him from reaching Trenzalore, the Doctor is eventually ready to accept his death. However, River breaks the suit's control over her and harmlessly discharges her weapon, breaking the "fixed point" and causing time to stall, all of history happening at once. To restore time, the Doctor offers to marry River, using it to reveal himself to be in the Teselecta so she can assist in killing him.
With only Amy and Rory knowing the truth after being left on Earth, an incarcerated River maintains the farce that she murdered the Doctor while he uses the opportunity to drop out of sight and erase any information related to himself. Feigning ignorance on her part in the Doctor's past, River assists him as a companion prior to her death in the "Silence in the Library"/"Forest of the Dead" two-part episode and had her eventual closure with the Doctor in "The Name of the Doctor". It would be during the events of "The Time of the Doctor", once at Trenzalore and encountering the Papal Mainframe that Kovarian was a member of, that the Doctor learns the reasons behind the attempts on his life by Kovarian and the Silence and that their actions were part of a bootstrap paradox to stop him from causing a new time war.
During the Eleventh Doctor's final series of adventures, Series 7 focused on the mystery behind Clara Oswald and the impossibility of her having multiple lives.
In "Asylum of the Daleks", the Doctor meets a woman called "Oswin Oswald" who has been turned into a Dalek by the inmates of a prison planet known as the Dalek Asylum. She dies, giving her life to save the Doctor, Amy and Rory when the Daleks destroy the asylum. Although the Doctor never saw her human face, he remembers her voice and love for making soufflés. She appears again in "The Snowmen", going by the first name "Clara", in Victorian London, and having no memory of their meeting. She manages to coax the Doctor out of the sulk he has been in since losing Amy and Rory in "The Angels Take Manhattan", and into resuming his adventures. She dies again, having been pulled from a great height by the Ice Governess, a creature brought to life by the evil Great Intelligence. The Doctor notices the resemblance to Oswin because of her love of soufflés, similar phrases, and her gravestone stating her full name – Clara Oswin Oswald.
Interested in finding out how someone can exist as separate, similar people in different points in time, the Doctor takes off to find a third version of Clara to take on as his companion. He succeeds in finding Clara in 2013 in "The Bells of Saint John" when she somehow obtained the phone number to his TARDIS, saving her from death this time. Over subsequent episodes, the Doctor's investigations repeatedly turn up evidence that Clara is just an ordinary girl. The mystery surrounding her appearances is resolved when she and the Doctor go to the site of his future burial in "The Name of the Doctor", where the Great Intelligence entered the Doctor's time stream and ceased to be while scattering himself across the Doctor's timeline to make him suffer. Clara follows into the time stream and, learning of the Doctor's meeting with previous Oswalds, realizes that they are some of the many echoes of herself that save the Doctor countless times over his lives. Luckily, the Doctor rescues Clara from his timeline and she later plays a role in the Doctor's new regeneration cycle in "The Time of the Doctor" and then in giving the Doctor his courage and ideals in "Listen".
In Series 8, the mystery of Clara obtaining the Doctor's phone number is revealed to be the Master's doing.
Since the end of the Eleventh Doctor's second series of adventures, it had been hinted that his end would soon come. The Silence's bungled attempts to kill the Doctor were to keep a prophecy from coming true – "On the fields of Trenzalore, at the fall of the eleventh, a question will be asked; a question that must never be answered." The question itself is "Doctor Who?"; due to the Doctor's time traveling, it is the oldest question in the universe. The Name of the Doctor also reveals that the Doctor is to die on Trenzalore in a great battle. But linked to both the cracks in the universe and the quote "Silence will fall", the Eleventh Doctor's journey has been influenced by the siege of Trenzalore where a Gallifreyian message from outside the universe attracted the attention of the Doctor's various enemies. With the Church of the Papal Mainframe attempting to maintain peace while intending not to have "the Time War begin anew", the Doctor remains on Trenzalore to defend the planet but not answering the question that would allow the Time Lords to return. But as he is revealed to be in his final incarnation, the Doctor ages over the centuries as only the Daleks remained after the siege turns into all-out war between them and the shattered remnants of the Papal Mainframe that resisted being taken over by the Daleks. However, as the Doctor is resigned to his fate, Clara asks the Time Lords to help him and in doing so she convinces them to give the Doctor a new regeneration cycle. This allows the Doctor to destroy the Dalek forces with the energy released as he eventually regenerates into the Twelfth Doctor.
In several episodes of series 8 of Doctor Who, characters who have died earlier turn up in a mysterious place to be greeted by a woman named Missy (Michelle Gomez) or her assistant Seb (Chris Addison) and told they are now in the Nethersphere, which is known by various names that include Heaven, Paradise, and the Promised Land. Even robotic beings from the distant future sought to find the location as depicted in the episodes Deep Breath and Robot of Sherwood.
The last two episodes of Series 8 ("Dark Water" and "Death in Heaven") show that this is an elaborate deception, and that Missy is the Master, who has escaped from Gallifrey and is now in female form. The Nethersphere is revealed to be a virtual reality in a Gallifreyan Matrix Data Slice that has been active since humanity first developed a notion of life after death. The Nethersphere is hidden in London's Saint Paul's Cathedral where Seb, revealed to be an artificial intelligence construct, manipulates the recently deceased into deleting their emotions before the minds are transferred back into their converted Cyberman bodies. Missy's plan is to convert all of humanity - living and dead - into a Cybermen army to be put at the Doctor's disposal. The Doctor declines, and Clara Oswald's recently deceased boyfriend Danny Pink, who was revived as a Cyberman, takes command of the Cybermen army and orders them to fly up high and all self-destruct, and thus to destroy the remainder of the Master's plan. Missy is once again apparently killed with the Nethersphere eventually shutting down.
Other story and character arcs comprise a number of other episodes across the programme's history:
Although not initially revealed in the series, following "The Two Doctors" – which showed older versions of the Second Doctor and Jamie McCrimmon working with the Time Lords, with the Second Doctor noting that he is officially an exile at this time – various fans and producers began to speculate that, after his trial in "The War Games", the Second Doctor was used as an agent for the Time Lords to carry out various missions that they didn't want to be seen doing themselves before he was officially made to begin his exile in "Spearhead from Space". The canonicity of this theory was initially confirmed as a flashback in the Sixth Doctor novel Players – which featured a flashback to an incident where the Second Doctor saved Winston Churchill from an attempt by mysterious time-travelers to send him to Germany in 1915, as either a prisoner or an 'official' traitor – and was later confirmed in World Game, where the Doctor acted to prevent his opponents altering the outcome of the Battle of Waterloo. Various short stories featuring a grey-haired Second Doctor are also speculated to take place in this time frame.
Created by Gary Russell in The Scales of Injustice, the Irish twins were Ciara and Cillian, twins enhanced by various Auton technology to act as assassins for a renegade government minister in his quest for power. Although the minister's first attempt was defeated by UNIT and the Third Doctor, his second attempt was more successful as he was manipulated into aiding the Nestene Consciousness into mounting a new invasion until he was defeated by the Sixth Doctor (Business Unusual). During this confrontation, the twins' programming was broken and their own minds restored, resulting in them joining forces with a powerful psychic in a quest for redemption and to stop a new invasion of Earth, concluding with them both dying saving the Doctor's companions Melanie Bush and Evelyn Smythe (Instruments of Darkness).
Conceived by Terrance Dicks, the Players were mysterious beings existing outside of time who manipulated human history as part of their games, often attempting to alter the outcome of crucial wars to see what would happen. During his encounters with them, the Second Doctor was forced to avert the Players' efforts to alter the outcome of the Napoleonic Wars and the Battle of Waterloo (World Game), the Sixth Doctor acted to protect Winston Churchill from the Players' attempts to kill him (during his third encounter, the Players also sought to ensure that King Edward VIII rose to the throne due to his sympathies with Hitler's policies (Players)), and the Eighth Doctor had to thwart the Players' attempts to escalate the Cold War into open conflict (Endgame). As of their last appearance, the Players remain potentially active, but have yet to encounter the Doctor again.
During the novel Cat's Cradle: Witch Mark, the Seventh Doctor repairs the recently damaged TARDIS with organic protoplasm from a semi-mystical realm, which results in the TARDIS being infected by a demonic parasite that goes on to disrupt the ship for the next few books, manipulating the Doctor's moods due to his psychic link to the ship, along with other symptoms such as the TARDIS's corridors extending to infinity and various malfunctions. The infection is eventually cured in Deceit, when the Doctor subconsciously reprogrammed the tertiary console to link itself to the Zero Room (Castrovalva), which was cut off from the outside Universe, allowing the Doctor to purge the infection from the ship without it knowing what he was doing as it could no longer read his mind and predict his attempts to get rid of it.
As part of the run-up to the show's thirtieth anniversary, the Virgin New Adventures did an 'Alternate Universe' series, featuring the Seventh Doctor, Ace and Benny dealing with an unknown foe attacking the Doctor by trying to change his history. This started when the TARDIS crash-landed on an alternate Earth where the Third Doctor was killed in his first encounter with the Silurians ("Doctor Who and the Silurians"), culminating in the Doctor being forced to destroy that universe in order to restore the energy taken from the original universe to create this one (Blood Heat). While tracking his new foe, the Doctor discovered that someone had changed his history in the real universe by preventing him averting the creation of the Garvond, a creature born from the Matrix (The Dimension Riders), was briefly bonded to a psychic manifestation of an Aztec warrior (The Left-Handed Hummingbird), found himself once again in the Land of Fiction ("The Mind Robber", Conundrum) before facing his enemy in 1970s London (No Future), his enemy being identified as old foe the Monk ("The Time Meddler").
This was a story arc in the Eighth Doctor's earliest Big Finish adventures. The Doctor rescues Charley Pollard from the R101 crash, creating a paradox, however he can't bear to put her back on the R101. There are then clues in the second season of the Eighth Doctor's Adventures to something being wrong with history. Invaders from Mars, set in 1938, has deliberate errors there are 49 states in the United States rather than 48, and the CIA is present despite not being formed till 1947. In The Chimes of Midnight the paradox of Charley's survival, combined with the suicide of Edith after Charley's death has created a time loop that leads to a house coming to life. In Seasons of Fear the Doctor finds the Nimon are trying to conquer Earth, which would create an alternate timeline where they are the masters of time. After averting this timeline he thinks the Nimon were responsible for the disturbances in time, but later learns that they just took advantage of pre-existing anomalies (Another referenced anomaly includes Benjamin Franklin being President of the United States).
Another clue is people not recognising Shakespeare quotes. The Time of the Daleks reveals William Shakespeare has been taken down a time fissure, creating an alternate timeline without Shakespeare, but the Doctor is able to undo this change and restore Shakespeare.
Neverland reveals Charley has become a gateway to the Antiverse, causing Anti-Time to infect the Universe. The Neverpeople, people erased from history by the Time Lords, plan to trick the Time Lords into allowing a casket of anti-time onto Gallifrey, which will infect the Eye of Harmony and destroy the Web of Time. However the Doctor materializes his TARDIS round the casket, saving the Web of Time. Charley helps him with this, as her existence saved the Web of Time the paradox and the resulting events become part of the Web of Time. The Doctor and TARDIS are infected by Anti-Time, the Doctor becoming violent and calling himself Zagreus, after a monster in Gallifreyan lore that represented Anti-Time. This leads into Zagreus.
Rassilon, founder of Time Lord Society, recruits the Zagreus-Doctor and Zagreus-TARDIS to destroy the Divergence, a race that would eventually eclipse the Time Lords, meaning Rassilon had imprisoned them in another Universe. However Zagreus refuses to obey Rassilon and hurls him into the Divergent Universe. Pure zero matter stabilizes the anti-time within the Doctor. However there is still Anti-Time present, causing him to be exiled to the Divergent Universe, where time travel isn't possible. Charley Pollard stows away on the TARDIS, the two eventually gaining a new companion in the form of C'rizz when they are briefly separated from the TARDIS and forced to travel through various different zones on the planet they landed on to find the ship once more. Having regained the TARDIS, it is revealed that the Anti-Time was removed from the Doctor by Rassilon when the Doctor entered the Divergent Universe, and Zagreus becomes a separate entity. Finally the Doctor leaves, with Rassilon remaining trapped in the time looped Universe with Zagreus.
After her departure from the Eighth Doctor (The Girl Who Never Was), Charley was unintentionally rescued by the Sixth Doctor when he responded to her distress call while she was trapped on Earth in 500,002 (The Condemned). Although initially content to travel with the Doctor again, Charley's attempt to conceal her future history with the Doctor made him increasingly suspicious. Eventually, Charley confessed the truth- along with her belief that the Eighth Doctor had died before she had left him- so that the Sixth Doctor would allow his memories of their time together to be altered to ensure that he would not recognize the younger Charley when they met (Blue Forgotten Planet). Charley left to help the Viyrans, while the Sixth Doctor moved on with no memory of his time with Charley Pollard, his memories altered so that Charley's face and name were replaced with someone else.
During the Eighth Doctor Adventures, the Eighth Doctor became aware of a mysterious War that would be waged in Gallifrey's future between the Time Lords and an initially-unidentified Enemy. Although the Doctor attempted to avoid learning too much about this War in case it affected his future, his first encounter with the War in Alien Bodies revealed that his final incarnation would die in the early stages of the War, forcing him to participate in an auction to buy his own corpse to prevent various races getting their hands on his unique biodata. After witnessing a weapon from the Future War nearly being used to destroy Earth (Interference: Books One and Two) and narrowly averting a Time Lord mission to release the Fendahl to use as a weapon in the War (The Taking of Planet 5), the Doctor learned that the Enemy were the ancestor cells, the cells from which all life evolved, roused to attack due to dimensional anomalies triggered by his own damaged TARDIS as it tried to save his life. Faced with a war that would dehumanize his people to the point of becoming monsters that all evidence suggested they couldn't win, the Doctor drained his ship of power to activate its ancient weapons systems, the resulting blast destroying Gallifrey and the Enemy fleet simultaneously, although he survived thanks to the aid of his companions (The Ancestor Cell).
In The Shadows of Avalon, the Doctor's TARDIS is destroyed in a dimensional rift, starting a chain of events that culminates in his companion Compassion being mutated into a Type-102 TARDIS, the 'mother' of TARDISes that will be used by the Time Lords in the Future War. Refusing to allow his companion to become a slave and breeding stock, the Doctor goes on the run with Compassion. Although the Doctor installed a Randomiser to try and help Compassion stay away from the Time Lords (The Fall of Yquatine), they were briefly trapped by an artron field (The Banquo Legacy) that allowed the Time Lords to find their next destination in The Ancestor Cell. The events of Cell ended with Compassion going her own way and the Doctor being left with his regenerating original TARDIS.
Between the events of The Ancestor Cell and Escape Velocity, the Eighth Doctor was stuck on Earth for the duration of the twentieth century, never aging and with no memory of his past as the TARDIS, drained of its power and reduced to a small black cube about an inch squared in size, began to slowly repair itself. During this time, the Doctor must defeat a mysterious fire elemental (The Burning), an attempt to harness the psychic grief of traumatized WWI soldiers (Casualties of War), prevent an attempted coup by a woman who believes herself to be the reborn Morgan le Fay (Wolfsbane; also features the Fourth Doctor, although neither Doctor is aware of the other), tackle a conspiracy with the aid of Alan Turing, Graham Greene and Joseph Heller (The Turing Test), prevent his old foes the Players from escalating the Cold War (Endgame) and protect his new adopted daughter Miranda from her family's old enemies (Father Time). The storyline concludes with the Doctor being reunited with his old companion Fitz Kreiner on 8 February 2001, shortly before the TARDIS finishes regenerating itself, leaving him free to wander through time and space once again.
With the destruction of the Time Lords, other time-active powers rise to fill the void left by their absence, as well as other races trying to take advantage. The most prominent individual to emerge in the post-Time Lord universe is Sabbath (The Adventuress of Henrietta Street), a master manipulator who sees himself as the Doctor's 'replacement'- regarding the Doctor as old, out-of-date and incapable of coping with the modern universe- attempting to manipulate the Doctor into furthering the agenda of his masters. However, Sabbath's plans eventually come to a halt when his actions endanger reality due to his flawed understanding of how time travel affects the universe, as he learns that he has been manipulated by an alien race known as the Council of Eight, posing as humanity's future with the goal of tricking Sabbath into collapsing the universe down to a single timeline that they can control. Sabbath defeats the Council- who gain power by predicting that events will happen and gaining energy from that prediction; reality was collapsed to a single timeline to ensure that their predictions would be accurate- by committing suicide when the Council's chairperson had predicted that Sabbath would kill him, the prediction being needed to power a weapon that would destroy human history and give the Council the power they needed to exist in the first place (Sometime Never...).
In Blood of the Daleks, first episode of the New Eighth Doctor Adventures, Lucy Miller, a woman from Blackpool 2006, suddenly appears on the TARDIS when she is meant to be starting her first day at work. The Doctor discovers the TARDIS can't travel to this location and can't travel without Lucie, part of a Time Lord Witness Protection Programme. Meanwhile a Headhunter is hired to capture Lucie Miller, following her through time. Lucie is finally captured by the Headhunter in No More Lies, which leads into Human Resources. The Time Lord Straxus appears and claims the Celestial Intervention Agency have been manipulating Lucie's life to prevent her turning into a right-wing dictator, however she got caught up in another Time Lord operation against the Cybermen. It is then revealed the wrong person had been taken, Karen, a girl interviewed on the same day as Lucie, was the real project of the CIA.
In various Big Finish dramas there were references to mysterious viruses, starting with Urgent Calls. The Viyrans first appeared in the Fifth Doctor audio Mission of the Viyrans, tracking down Virus 7001, which has infected the Doctor's companion Peri and mutates people into patient zero. Patient Zero finally revealed why the Viyrans were tracking down the viruses; various strange viruses were collected on the Amethyst Viral Containment Station in the distant past, but a Dalek invasion and the unintentional interference of the Sixth Doctor resulted in an explosion which scattered the viruses through space and time before the Viyrans could destroy them. The Viyrans therefore dedicate themselves to retrieving and destroying the viruses. This arc carries over into Blue Forgotten Planet (Where the Viyrans' actions nearly destroyed humanity in their effort to contain a virus before the Sixth Doctor found a cure and a means of undoing the damage they had done), Lucie Miller and Dark Eyes 2.
In Patient Zero the Dalek Time Controller appears, a Dalek from the far future who is the strategist of Dalek time missions, and is leading a Dalek squad to capture the Amethyst Viruses, which have been traced to the Amethyst Viral Containment Station. The Sixth Doctor accidentally causes it to realise these events are a time loop, the explosion at the station will scatter the viruses, causing the Daleks to trace them back to the station. It allows the explosion to happen and the Doctor thinks it is destroyed.
However in Lucie Miller/To the Death it is revealed the Dalek Time Controller was hurled back in time by the explosion and is retrieved by the Daleks. While in the Time Vortex it saw the point in history where the Amethyst Viruses would converge. It masterminds another Dalek invasion of Earth in the 22nd century and plans to install a Time Warp Engine in Earth, enabling the Daleks to pilot it to that point and make it a plague planet. The Daleks will then pilot Earth through time and space and with the plagues destroy any world that comes under Earth's influence. However Lucie Miller foils this plan by crashing a Dalek Saucer into the mine, sacrificing herself but causing the Daleks, including the Time Controller, to be sucked into a time warp.
The Dalek Time Controller returns in Dark Eyes, having been rescued by the Time Lord Kotris. Together they plan to destroy the Time Lords. The Eighth Doctor foils this plan and when the Time Controller exterminates Kotris' previous incarnation Straxus these events are erased from history.
The Dalek Generation by Nicholas Briggs depicts the Time Controller first encountering the Doctor, though this is the Eleventh Doctor. The Time Controller's plan to turn the Sunlight Worlds into copies of Skaro is foiled but it escapes.
Dark Eyes 2 reveals the Time Controller has retained its memory of these events and is commanding the Daleks on Nixyce VII. However the Eighth Doctor works with it to combat the Eminence.