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    Doctor Who (Original Series, 1963-1989) 
  • First Doctor (Seasons 1-4): The Daleks make their debut in Season 1 and quickly establish themselves as the Doctor's Arch-Enemies by the second season, invading and enslaving the people of Earth before directly hunting down the TARDIS. In Season 3 they notably serve as the main antagonists of the twelve-part serial "The Daleks' Master Plan," working with Mavic Chen and the Galactic Council to construct a Time Destructor before betraying them to conquer the solar system.
    • There's also the Meddling Monk, who is introduced at the close of season two and is the first member of the Doctor's race that he crosses swords with, as the Monk tampers with established history in order to "improve" things. However, his status as an Ineffectual Sympathetic Villain is confirmed when he attempts to get revenge on the Doctor only to collide with the Daleks' latest scheme: He is hopelessly outclassed and quickly flees the scene.

  • Second Doctor (Seasons 4-6): The Cybermen are the most prominent foes of this era, replacing the Daleks as the Doctor's arch-enemies in Season 5 and concocting various schemes to conquer the Earth or bolster their power.
    • Season 4 has the Daleks, who are the Second Doctor's first opponents before returning in season finale, which sees the Doctor facing the Dalek Emperor.
    • Season 5 also has the Great Intelligence, who faces the Second Doctor twice over the course of the season.

  • Third Doctor (Seasons 7-11): The Master is the mastermind behind almost every conflict during the Third Doctor's tenure. His schemes range from working with other races to Take Over the World, uncovering an ancient super-weapon, unleashing the chronovore Kronos to usurp the throne of Atlantis, and instigating a war between Earth and Draconia on behalf of the Daleks. While the Master's schemes occasionally backfire and he has to work with the Doctor to undo the damage, he always escapes to cause trouble later.
    • Season 10-11: The Daleks, who following their return in Season 9 are revealed a pair of linked six-parters to be the True Final Boss behind the Master, employing him to start an interstellar war, and even when he is defeated, they still plan to go ahead with their invasion using a frozen army of 10,000 Daleks. They later travel to Exxilon to get control of the only cure for a space plague and use it to hold the governments to ransom.

  • Fourth Doctor (Seasons 12-18): The Master and Davros, with the former returning to try and secure a new body for himself, while the latter is revealed to be the creator of the Daleks, who is later reawakened by his creations to assist them in their war with the Movellans.
    • Season 15 has the Sontarans, who are indirectly responsible for Rutan invasion in the Season 15 premiere before returning in the finale, where they're revealed to be using the Vardans as patsies for their invasion of Gallifrey.
    • Season 16 (The Key to Time): The Black Guardian, the Evil Counterpart of the White Guardian and the anthropomorphic representation of evil itself, who seeks to assemble the titular Key.

  • Fifth Doctor (Seasons 19-21): The Master (having secured a new body for himself by possessing the body of Tremas) is the most prominent foe of the Fifth Doctor's era, orchestrating various schemes to wreak havoc or simply to get revenge on the Doctor.
    • Season 20: The Black Guardian, who has returned to get revenge by having Turlough join the Doctor in order to assassinate him.
    • "The Five Doctors": Although previously appearing as an ally to the Doctor, Lord President Borusa is the real mastermind, sending the Doctors to disable the defences of the Tomb of Rassilon so he can achieve immortality.

  • Sixth Doctor (Seasons 21-23):
    • Season 23 (Trial of a Time Lord): The Valeyard is the prosecutor of the Doctor's trial, hired by the Time Lord High Council to execute him before he can discover their accidental near-genocide of Earth in the future. The Valeyard eventually betrays his employers and is revealed to be a future amalgamation of the Doctor's darker sides, hoping to take his past self's regenerations. Even the Master forms an Enemy Mine with the Doctor to help against the Valeyard.

  • Seventh Doctor (Seasons 24-26): It turns out various events were the doing of Fenric, an Ancient Evil from the dawn of time who was imprisoned by the Doctor. He manipulates the timeline from within his prison to ensure his release, notably transporting Ace to Iceworld so she can be used as a weapon against the Doctor in the future.

  • Eighth Doctor (The TV Movie): The new incarnation of the Master crashes the TARDIS and opens the Eye of Harmony, damaging the fabric of reality in his plan to steal the Doctor's remaining regenerations.

    Doctor Who (Revival Series, 2005-present) 
  • Series 1: The Dalek Emperor, whose leadership of the Daleks during the Time War played a major role in the state of the universe by the time of the beginning of the new show and left the Doctor freshly traumatized, and who's been playing the "long game" behind the scenes to create a new army of Daleks.

  • Series 2: A Big Bad Ensemble between the Cybus Cybermen, Cybermen created by a Corrupt Corporate Executive on a parallel earth, and the Cult of Skaro, an elite group of Daleks led by Dalek Sec. The former serve as the main antagonists of a two-parter and invade the Doctor's world in the finale, while the latter opened the breach between the two worlds to release the millions of Daleks imprisoned in the Genesis Ark before quickly eclipsing the Cybermen in threat.

  • Series 3: The "Harold Saxon" incarnation of the Master, who converts the remnants of humanity from a Bad Future into bloodthirsty Toclafanes before using them to conquer present Earth, with the intent to then wage war on the entire universe.

  • Series 4: Davros, who's the driving force behind the Daleks' scheme to create the Reality Bomb and use it to destroy all of existence save for the Daleks. He's technically the "pet" for the Supreme Dalek, but is still the face of the Dalek threat.

  • 2009 Specials: Lord President Rassilon, who used the Master as a pawn in a grand plot to prevent Gallifrey's fate in the Time War by destroying time itself.

  • Series 5: The New Paradigm Daleks, who blame the Doctor for causing the cracks in time that threaten to collapse reality and assemble an Alliance of his various enemy races to seal him in the Pandorica. The Silence are the true cause of the cracks, but are Greater-Scope Villains who don't appear until next season.

  • Series 6: The Silence and Madame Kovarian, who were responsible for destroying the TARDIS in the last season, and who are behind his death at the start of this season. The Silence's plotting actually encompasses the entirety of the Eleventh Doctor's Myth Arc, but they are not formally revealed in Series 5 and are absent in Series 7, only returning in his Grand Finale Christmas Episode.

  • Series 7: The Great Intelligence, in what is technically its first encounter of the Doctor before its encounter with him in classic series. It later sets out for revenge after the Doctor, scattering itself throughout time in an effort to undo all of the Doctor's victories.

  • 2013 Specials ("The Day of the Doctor" & "The Time of the Doctor"): The Daleks were Gallifrey's primary enemies during the Time War, which saw the Doctor seemingly destroy his own people in order to save the rest of the universe from both sides' bloody conflict. In the present, the Daleks (led once more by the New Paradigm's Supreme, as confirmed in supplementary material) are the most persistent force out to prevent the Time Lords' return by killing the Doctor before he can summon them from Trenzalore, even converting the Church of the Papal Mainframe—the organization that Kovarian split from in order to pursue her own violent campaign against the Doctor, unwittingly creating the same cracks in the universe the Time Lords now threaten to return from in the process—into Dalek puppets.

  • Series 8: The Mistress, or "Missy", incarnation of the Master, whose plot to create an army of Cybermen from the dead spans the season before coming to a head in the finale. For bonus points she also had a hand in the events of Series 7B by getting the Doctor together with Clara Oswald.

  • Series 9: Rassilon, orchestrating a gambit to lure the Doctor to Gallifrey so he can imprison the Doctor in his confession dial and interrogate him. Although in the finale the Doctor deposes him and temporarily becomes a Villain Protagonist when his grief and efforts to save Clara create a paradox that threatens the universe.

  • Series 10: The Saxon Master returns as The Heavy, orchestrating the genesis of the Mondasian Cybermen to upgrade Bill, torture the Doctor, and stop Missy's Heel–Face Turn. However, the Doctor reprograms his Cybermen to include Time Lords in their definition of those who must be upgraded, forcing the Masters into an Enemy Mine with him to escape the Cybermen's subsequent betrayal. The Cybermen proceed to serve as the main antagonists of the finale, launching endless sieges to upgrade the surviving humans on their ship.

  • Series 11: Tzim-Sha is a Stenza warrior and the Thirteenth Doctor's Starter Villain whose ritualistic hunt to claim leadership of his people results in Grace's death. He returns in the finale posing as the god of the Ux, stealing planets to power a superweapon he intends to use on Earth as revenge for his earlier defeat.

  • Series 12: A Big Bad Ensemble between "The Lone Cyberman" Ashad and the "Spy" Master. The former, a misanthrope who willingly let himself be partially upgraded, tracks down the collective knowledge of the Cybermen held within the Cyberium to build a Death Particle that can wipe out all organic life; the latter massacres Gallifrey after learning the Dark Secret of the Timeless Child and infiltrates MI6 to facilitate a Kasaavin invasion, later killing Ashad to steal the Cyberium and create an army of Time Lord "CyberMasters."

  • Series 13 (Flux): A Big Bad Ensemble between the Sontarans and the Ravager twins, Swarm & Azure. The former, led by Commander Stenck, ally with an exiled galactic dictator known as the Grand Serpent to conquer the universe in the aftermath of the titular Flux; the latter seek to destroy the universe and unravel the linear restraints of their master, Time itself. Tecteun, the Doctor's adoptive mother and head of Division, is the Greater-Scope Villain who unleashed the Flux onto the universe after coming to view it as a failed experiment, but she's killed by Swarm when he hijacks the Flux for his own omnicidal purposes.

  • 2022 Specials (primarily "The Power of the Doctor"): The Master unites the Daleks and his CyberMasters to wipe out humanity. All this is done as part of a larger gambit to capture his nemesis and force her through a regeneration, with the Master intending to use the process to steal their body and commit atrocities in their name.

  • 2023 60th Anniversary Specials (primarily "The Giggle"): The Toymaker, returning many years after his battle with the First Doctor, is accidentally released into the universe in the second of the specials. The godlike entity wastes no time using his newfound freedom to begin playing apocalyptic "games", intending to use humanity as his new toys for eternity.

    Other Shows 
  • Torchwood:
    • Series 1: Abaddon is the demonic Son of the Beast, released from his prison in the rift by his time-travelling servant, Bilis Manger.
    • Series 2: Gray, Jack's brother, seeks revenge after being abandoned during an alien invasion and forced into a life of servitude. Jack's ex-boyfriend, Captain John Hart, is forced into becoming The Dragon.
    • Children of Earth: The 456 are an alien race who invade Earth, with their Ambassador threatening to wipe out humanity unless they're given a tenth of the planet's children to be harvested for euphoric drugs.
    • Miracle Day: The Three Families are the descendants of a group of men from the 1920’s who stole Jack’s blood, using it in the modern day to end death and subsequently cause mass chaos.

  • The Sarah Jane Adventures:
    • Series 1: A Big Bad Duumvirate between the Slitheen and Mr. Smith. The former seek revenge after a previous scheme to drain the Earth's energy and take over their homeworld was foiled. The latter is a member of the Xylok race, acting as Sarah Jane's supercomputer while plotting to drag down the moon and destroy the planet to free his people.
    • Series 2: Mrs. Wormwood is a Bane who created Luke, seeking to release the immortal entity Horath to conquer the universe and make up for her previous failure. Commander Kaagh is a Sontaran who wants to destroy Earth in order to avenge his fleet, teaming up with Wormwood to do so.
    • The Trickster is an extra-dimensional entity, causing chaos by altering the timeline. He appears in each of the first three seasons, creating a temporal disruption that requires the sacrifice of someone close to Sarah (her childhood best friend, her parents and her new fiance) to put right. It was intended to be revealed at the climax of Series 5 that he was gradually possessing Sky to gain corporeal form, but the death of Elisabeth Sladen led to the season being discontinued. The Trickster makes his return in the dubiously canonical internet webisode Farewell Sarah Jane, infiltrating Sarah Jane’s memorial with the intent of replacing the Earth with a duplicate from another universe.

  • Class (2016): Corakinus is King of the Shadow Kin, responsible for the genocide of both the Rhodia and the Quill in pursuit of the Cabinet of Souls. The Board of Governors are the Greater Scope Villains, in service to the Weeping Angels.

Audio

    Big Finish Productions 

  • The villains for the Eighth Doctor's stories before the Divergent Universe Arc are the Neverpeople, then Rassilon. The villain for the Divergent Universe arc seem to be the Divergents, working through the Kro'ka. However by the finale it turns out the Divergents have died and Rassilon is really the Kro'ka's boss.
  • The Headhunter in the "New Eighth Doctor Adventures" Series 1, though Mr Hulbert, who hired her, could be considered this.
  • The Meddling Monk in the New Eighth Doctor Adventures Series 4, though at the end he is eclipsed by the Daleks, led by the Dalek Time Controller.
  • Then the Dalek Time Controller becomes this for "Dark Eyes", though Kotris may hold this role.
  • In "Dark Eyes 2" the Eminence, who are so dangerous the Doctor even works with the Dalek Time Controller against them. However the Master could also be considered this.
  • The Forge, under the leadership of Nimrod during the Forge trilogy (Project: Twilight, Project: Lazarus and Project: Destiny), though they influence a lot of factors throughout 6th and 7th Doctor's Monthly Range stories including: the remnants of their experiments with vampires causing Cassandra Schofield's vampirism in "Project: Twilight", the rebuilt organization causing her death later on in "Project: Lazarus", leading to a wedge to be driven in Evelyn Smythe's and 6th Doctor's relationship, directly causing the events of Vilag duology ("Arrangements for War" and "Thicker Than Water"), as well as influencing 7th Doctor's choice in picking up Thomas "Hex" Schofield as his companion in The Harvest. From there, the 7th Doctor encounters the Forge several times across his travels into 20th century, including "No Man's Land" and "Casualties of War" in anthology set "Forty Five", before concluding the arc in "Project: Destiny" with Nimrod's seeming demise. Furthermore, during events of "Death in the Family", in a talk with Evelyn, 7th Doctor implies that his battles against the Forge and Cassandra's death are a major reason for his Chessmaster character
  • The Dalek Time Squad in the "Time Lord Victorious" trilogy for the 8th Doctor portion of the multi-media event, lead by Dalek Time Commander, though Dalek Prime Strategist betrays and teams back up with both them and the Doctor on several occasions throughout the trilogy.

Prose

    Virgin New Adventures 
  • The New Adventures: The Timewyrm tetralogy has the Timewyrm. The Alternate Universe Cycle has the Meddling Monk. The Psi Powers arc has the Brotherhood, ultimately led by the Grandmaster.

    Eighth Doctor Adventures 
  • The Faction Paradox storyline has Grandfather Paradox, although he's more of a Greater-Scope Villain. The Compassion arc has Romana of all people, seeking to capture Compassion in order to improve the Time Lords' TARDIS technology. The Sabbath arc has the Council of Eight, especially Octan.

    Others 
  • Crossovers: The New Adventure "Blood Harvest" sets up Lord Yarven as the Big Bad of the first Missing Adventure "Goth Opera". The Missing Adventure "The Scales of Injustice" and the Past Doctor Adventure "Business Unusual" have Martin Townsend (AKA "the pale man") as the Big Bad.

Others

    Others 

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