History BigBad / Whoniverse

* First Doctor (Seasons 1-4): The Daleks make their debut in Season 1 and quickly establish themselves as the Doctor's [[ArchEnemy Arch-Enemies]] by the second season, invading and enslaving the people of Earth before directly hunting down the TARDIS. In Season 13 they notably serve as the main antagonists of the twelve-part serial "[[Recap/DoctorWhoS3E4TheDaleksMasterPlan 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.

** Season 4 has the Daleks, who are the Second Doctor's first opponents with their attempt to take over the human colony on Vulcan and massacre the colonists. The season finale sees the Doctor facing the Dalek Emperor, who kidnapped the Doctor in a plan to [[XanatosSpeedChess either]] give the Daleks human traits to make them more powerful or mentally transform all humans to Daleks.
** Season 5 also has the Great Intelligence, who becomes a major villain after its [[Recap/DoctorWho2012CSTheSnowmen first encounter with the Doctor]], possesses High Lama Padmasambhava and commands robotic Yeti to scare off intruders while it creates a corporeal form for itself. It later tries to drain the Doctor's mind.

** The Third Doctor's tenure also sees the return of Daleks, who first show up at the start of Season 9, having changed history so they have occupied Earth for a hundred years by the 22nd century, before a pair of linked six-parters in Season 10 see them revealed as the TrueFinalBoss [[TheManBehindTheMan 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.

** The Master, although he spends part of it in a BigBadDuumvirate with another Time Lord, the Rani, to hijack the Industrial Revolution while she continues her experiments on the populace.

* 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 and ascending the Time Lords all to beings of pure consciousness.

* Series 6: The Silence, who believe the Doctor will pose a threat to the entire universe in the future, with Madame Kovarian acting as [[TheHeavy the face]]. They destroyed the TARDIS in the future, consequently creating the cracks in time, and kidnap Amy to raise her daughter to one day assassinate the Doctor.

* Series 8: The Mistress, or "Missy", incarnation of the Master collects deceased people from throughout history to resurrect as Cybermen. She uses them to disperse "cyberpollen" into the atmosphere and raise more Cybermen from graveyards across the globe, intending to slaughter and then upgrade the rest of humanity into an army as a gift for the Doctor.

* Series 9: Rassilon, who is indirectly responsible for [[spoiler:Clara's death]] and who imprisons the Doctor in the confession dial. [[spoiler:Although in the finale the Doctor deposes him and temporarily becomes a VillainProtagonist when his grief and efforts to save Clara create a massive paradox that threatens the universe.]]

** Season 4: The Daleks are the Second Doctor's first opponents, first attempting to take over the human colony on Vulcan and massacre the colonists. The season finale sees the Doctor facing the Dalek Emperor, who kidnapped the Doctor in a plan to [[XanatosSpeedChess either]] give the Daleks human traits to make them more powerful or mentally transform all humans to Daleks.
** Season 5: The Great Intelligence becomes a major villain after its [[Recap/DoctorWho2012CSTheSnowmen first encounter with the Doctor]], possesses High Lama Padmasambhava and commands robotic Yeti to scare off intruders while it creates a corporeal form for itself. It later tries to drain the Doctor's mind.

* Series 3: The "Harold Saxon" incarnation of the Master, who--after regaining his old memories--converts the remnants of humanity from a BadFuture into bloodthirsty Toclafanes. He proceeds to travel to the present to get himself elected Prime Minister, before then summoning his forces from the future to first TakeOverTheWorld and then wage war on the entire universe.

* Series 4: Davros, who's the driving force behind the Daleks' scheme even though he's technically the "pet" of the new Supreme Dalek, plotting to create the Reality Bomb and use it to destroy all of existence save for the Daleks.

* 2009 Specials ("[[Recap/DoctorWhoS30E17E18TheEndOfTime The End of Time]]"): The Master at first, only for him to turn out to be being manipulated by Lord President Rassilon, who drove him insane in a plot to use him to escape his fate in the Time War so he can destroy time and ascend the Time Lords to beings of pure consciousness.

* First Doctor (Seasons 1-4): The Daleks make their debut in Season 1 and quickly establish themselves as the Doctor's [[ArchEnemy Arch-Enemies]] by the second season, invading and enslaving the people of Earth before directly hunting down the TARDIS. They notably serve as the main antagonists of the twelve-part serial "[[Recap/DoctorWhoS3E4TheDaleksMasterPlan 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.

* Second Doctor (Seasons 4-6): The Cybermen are the most prominent foes of this era, first with their plot to hijack the Graviton and destroy life on Earth, later planning to invade the planet again after the Cyber-Controller is awakened from his tomb on Telos. The Cyber-Planner orchestrates the takeover of the Wheel so it can be converted into a beacon for their fleet, while another Planner works with Tobias Vaughn to broadcast a hypnotic signal that will immobilize Earth's population.
** Season 4: The Daleks are the Second Doctor's first opponents, as a small number are innocently revived by the human colony on Vulcan, after which they bide their time and increase their numbers until they are ready to massacre the colonists. Under the direction of the Dalek Emperor, they later kidnap the Doctor to [[XanatosSpeedChess either]] give the Daleks human traits to make them more powerful or mentally transform all humans to Daleks.

** The Daleks return at the start of Season 9, having changed history so they have occupied Earth for a hundred years by the 22nd century, enslaving its population. A pair of linked six-parters sees them revealed as the TrueFinalBoss [[TheManBehindTheMan behind]] the Master, 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, now on his final, decaying regeneration, assassinates the Time Lord President to steal the Eye of Harmony and gain a new regeneration cycle. When that fails he steals the body of Traken scientist Tremas, before attacking Logopolis and accidentally setting off the heat death of the universe. The Master proceeds to work with the Doctor to stop the oncoming entropy, but betrays and kills him to blackmail the universe into accepting his rule.
** Davros is revealed as the creator of the Daleks, taking advantage of the war with the Thals to exterminate his rivals and eventually the remainder of the Kaled race. After being placed in suspended animation for thousands of years he awakens to take command of the Daleks, assisting them in their war with the Movellans.
** The Sontarans, a clone race bred for war, first plague the Fourth Doctor when they use a deserted future Earth to conduct experiments on humans prior to an invasion of the galaxy. They are indirectly responsible for Rutan invasion in the Season 15 premiere, then appear again in the finale, using the Vardans as patsies for their invasion of Gallifrey.

* Fifth Doctor (Seasons 19-21): The "Tremas" Master continues to wreak havoc, creating the town of Castrovalva to kill the recently-regenerated Doctor. He later causes a malevolent schism in the Xeraphin HiveMind after being stranded on Earth, tries to prevent the creation of the Magna Carta, and schemes to enter the Tomb of Rassilon.
** Season 20: The Black Guardian retakes the role for a trilogy of serials, having Turlough join the Doctor in order to assassinate him.
** "[[Recap/DoctorWho20thASTheFiveDoctors The Five Doctors]]": Lord President Borusa sends the Doctors to disable the defences of the Tomb of Rassilon, one of the founders of the Time Lords, so he can achieve immortality.

** 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.
** The Master works with another Time Lord, the Rani, to hijack the Industrial Revolution while she continues her experiments on the populace. He later returns in an EnemyMine to help the Doctor against the Valeyard.

* Seventh Doctor (Seasons 24-26): Fenric is an AncientEvil 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.

* Series 1: The Dalek Emperor led the Daleks during the Time War, a catastrophic conflict that has left the Doctor freshly traumatized at the beginning of the new show. Having survived the war and gone completely mad, the Emperor silently took control of Earth in a BadFuture, using the news channels and {{Immoral Reality Show}}s of Satellite Five as a front to acquire humans who can be mutated into a new army of Daleks.

* Series 4: Davros, even though he's technically the "pet" of the new Supreme Dalek, is the one directing the Daleks in stealing planets to construct the Reality Bomb so that they can destroy all of existence save for themselves.

* 2009 Specials ("[[Recap/DoctorWhoS30E17E18TheEndOfTime The End of Time]]"): Lord President Rassilon is revealed to be behind the drumming that drove the Master insane, intending to use him to escape his fate in the Time War so he can destroy time and ascend the Time Lords to beings of pure consciousness. The Master himself is TheHeavy after being resurrected by his cult, devouring humans to sate his hunger and turning everyone on Earth into clones of himself before Rassilon manipulates him into opening a portal to the time-locked Gallifrey.

* Series 5: The Silence are the [[GreaterScopeVillain Greater-Scope Villains]] who destroy the TARDIS in the future, consequently creating cracks in time that threaten to collapse reality. However, due to their physical absence, the closest things to proper [[TheHeavy overarching antagonists]] are instead the New Paradigm Daleks, who blame the Doctor for causing the cracks and assemble an [[LegionOfDoom Alliance]] of his various enemy races to seal him in the Pandorica.

* Series 6: The Silence, believing that the Doctor will pose a threat to the entire universe in the future, kidnap Amy and raise her daughter to one day assassinate him. Madame Kovarian is TheHeavy as the apparent leader of their faction and the one responsible for kidnapping Melody, but she's killed by the Silent Priests in the finale once she [[YouHaveOutlivedYourUsefulness outlives her usefulness]].

* Series 7: The Great Intelligence is a being of pure thought that first comes to Earth in the form of living snow, mirroring the subconscious thoughts of a resentful, Victorian-era man named Simeon before evolving into a distinct entity. It sets out for revenge after the Doctor foils several of its schemes to take over the world, scattering itself throughout time in an effort to undo all of the Doctor's victories.

* Series 9: Rassilon is indirectly responsible for [[spoiler:Clara's death]] and imprisons the Doctor in the confession dial, ostensibly to interrogate him about the prophesized [[TheDreaded Hybrid]]. The Doctor [[BigBadWannabe easily deposes him]] after escaping, but temporarily becomes a VillainProtagonist when his grief and efforts to [[spoiler:save Clara]] create a massive paradox that threatens the universe.

* Series 2: A BigBadEnsemble between the Cybus Cybermen, Cybermen created by a CorruptCorporateExecutive 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 [[Recap/DoctorWhoS28E5RiseOfTheCybermen two]]-[[Recap/DoctorWhoS28E6TheAgeOfSteel 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 and quickly eclipse the Cybermen in threat.

* 2022 Specials ("[[Recap/DoctorWho2022CENThePowerOfTheDoctor 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 [[spoiler:capture his nemesis and force her through a regeneration, with the Master intending to use the process to [[GrandTheftMe steal their body]] and commit atrocities in their name.]]

* 2023 Specials ("[[Recap/DoctorWho60thASTheGiggle The Giggle]]"): The Toymaker, returning many years after his battle with the First Doctor, begins playing apocalyptic "games" after being accidentally released into the universe, intending to use humanity as his new toys for eternity.

* Series 1: The Dalek Emperor. He controls Earth from the shadows in a BadFuture, using the news channels and {{Immoral Reality Show}}s of Satellite Five as a front to acquire humans who can be mutated into new Daleks.

* Series 3: The "Harold Saxon" incarnation of the Master, who after regaining his old memories converts the remnants of humanity from a BadFuture into bloodthirsty Toclafanes before traveling to the present to get himself elected Prime Minister, proceeding to summon his forces from the future to first TakeOverTheWorld and then wage war on the entire universe. The Cult of Skaro also return as {{Arc Villain}}s for a [[Recap/DoctorWhoS29E4DaleksInManhattan two]]-[[Recap/DoctorWhoS29E5EvolutionOfTheDaleks parter]], experimenting with humans to create [[HalfHumanHybrid Dalek hybrids]].

* Series 4: Davros, even though he's technically the "pet" of the new Supreme Dalek, is the one directing the Daleks in stealing planets to construct the Reality Bomb and destroy all of existence save for the Daleks.

* 2013 Specials ("[[Recap/DoctorWho50thASTheDayOfTheDoctor The Day of the Doctor]]" & "[[Recap/DoctorWho2013CSTheTimeOfTheDoctor The Time of the Doctor]]"): The Daleks were Gallifrey's primary enemies during the Time War, and are the most persistent force out to prevent the Time Lords' return by killing the Doctor before he can summon them from Trenzalore. The Church of the Papal Mainframe are initially the most prominent force opposing a renewed Time War, but are killed and turned into Dalek puppets; additionally, Kovarian and her Silent Priests are retroactively revealed to be a RenegadeSplinterFaction of the Church, [[StableTimeLoop who created the same cracks in the universe the Time Lords now threaten to return from]] in their efforts to ensure the Doctor's "silence."

* Series 9: Rassilon is indirectly responsible for [[spoiler:Clara's death]] and imprisons the Doctor in the confession dial, ostensibly to interrogate him about the prophesized [[TheDreaded Hybrid]]. The Doctor [[BigBadWannabe easily deposes him]] after escaping, but temporarily becomes a VillainProtagonist when his own grief threatens the universe as he creates a massive paradox [[spoiler:to save Clara]]. The opening [[Recap/DoctorWhoS35E1TheMagiciansApprentice two]]-[[Recap/DoctorWhoS35E2TheWitchsFamiliar parter]] features a dying Davros as the ArcVillain tempting the Doctor into either committing genocide on the Daleks or providing them access to his regeneration energy, with Missy as a WildCard alternating between helping the Doctor and trying to kill Clara.

* Series 10: [[spoiler:The Saxon Master returns as TheHeavy, orchestrating the genesis of the Mondasian Cybermen to upgrade Bill, torture the Doctor, and stop Missy's HeelFaceTurn. However, the Doctor reprograms his Cybermen to include Time Lords in their definition of those who must be upgraded, forcing the Masters into an EnemyMine with him to escape the Cybermen's subsequent betrayal.]]

* Series 11: Tzim-Sha is a Stenza warrior and the Thirteenth Doctor's StarterVillain 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 [[RealityWarper Ux]], stealing planets to power a superweapon he intends to use on Earth as revenge.

* Series 12: A BigBadEnsemble between "The Lone Cyberman" Ashad and [[spoiler: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 and wipe out all organic life; the latter [[spoiler:massacres Gallifrey after learning the DarkSecret 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=]."]]

* 2022 Specials ("[[Recap/DoctorWho2022CENThePowerOfTheDoctor The Power of the Doctor]]"): The Master unites the Daleks and his [=CyberMasters=] to wipe out humanity as part of a larger gambit to [[spoiler:capture his nemesis and force her through a regeneration, intending to use the process to [[GrandTheftMe steal their body]] and commit atrocities in their name.]]

* First Doctor (Seasons 1-4): The Daleks are introduced as a xenophobic race from Skaro, genetically engineered from the Kaled race in their war against the Thals. They quickly establish themselves as the Doctor's [[ArchEnemy Arch-Enemies]], invading and enslaving the people of Earth before directly hunting down the TARDIS. They notably serve as the main antagonists of the twelve-part serial "[[Recap/DoctorWhoS3E4TheDaleksMasterPlan 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.
** The Meddling Monk 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 IneffectualSympatheticVillain is confirmed when he attempts to get revenge on the Doctor only to [[CollidingCriminalConspiracies collide with]] the Daleks' latest scheme: He is hopelessly outclassed and quickly [[VillainExitStageLeft flees the scene]].

* Second Doctor (Seasons 4-6): The Cybermen are a race from Earth's twin planet of Mondas who replaced their bodies with mechanical parts to remove emotional weaknesses. They plot to hijack the Graviton and destroy life on Earth, later planning to invade the planet again after the Cyber-Controller is awakened from his tomb on Telos. The Cyber-Planner orchestrates the takeover of the Wheel so it can be converted into a beacon for their fleet, while another Planner works with Tobias Vaughn to broadcast a hypnotic signal that will immobilize Earth's population.
** Season 4: The Daleks are the Second Doctor's first opponents, as a small number are innocently revived by the human colony on Vulcan, after which they bide their time and increase their numbers until they are ready to massacre the colonists. Under the direction of the Dalek Emperor, they later kidnap the Doctor to [[XanatosSpeedChess either]] give the Daleks human traits to make them more powerful or mentally transform all humans to Daleks. They are apparently wiped out when the Doctor triggers a [[EnemyCivilWar civil war]] between the humanised Daleks and the originals.
** Season 5: The Great Intelligence, after its [[Recap/DoctorWho2012CSTheSnowmen first encounter with the Doctor]], possesses High Lama Padmasambhava and commands robotic Yeti to scare off intruders while it creates a corporeal form for itself. It later tries to drain the Doctor's mind.

* Third Doctor (Seasons 7-11): The Master, another renegade Time Lord stranded on Earth by the Doctor, is the mastermind behind almost every conflict during the Third Doctor's tenure. His schemes range from working with other races to TakeOverTheWorld, 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.
** The Daleks return at the start of Season 9, having changed history so they have occupied Earth for a hundred years by the 22nd century, enslaving its population. A pair of linked six-parters sees them revealed as the TrueFinalBoss behind the Master, 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.

* Series 1: The Dalek Emperor controls Earth from the shadows in a BadFuture, using the news channels and {{Immoral Reality Show}}s of Satellite Five as a front to acquire humans who can be mutated into new Daleks.

* Series 2: A BigBadEnsemble between the Cybus Cybermen and the Cult of Skaro. The former are Cybermen created by a CorruptCorporateExecutive on a parallel earth who, after serving as the main antagonists of a [[Recap/DoctorWhoS28E5RiseOfTheCybermen two]]-[[Recap/DoctorWhoS28E6TheAgeOfSteel parter]], invade the Doctor's world in the finale. The latter are an elite group of Daleks, led by Dalek Sec, who opened the breach between the two worlds to release the millions of Daleks imprisoned in the Genesis Ark, quickly eclipsing the Cybermen in threat.

* Series 3: The "Harold Saxon" incarnation of the Master, after regaining his old memories, converts the remnants of humanity from a BadFuture into bloodthirsty Toclafanes before traveling to the present to get himself elected Prime Minister, proceeding to summon his forces from the future to first TakeOverTheWorld and then wage war on the entire universe. The Cult of Skaro also return as {{Arc Villain}}s for a [[Recap/DoctorWhoS29E4DaleksInManhattan two]]-[[Recap/DoctorWhoS29E5EvolutionOfTheDaleks parter]], experimenting with humans to create [[HalfHumanHybrid Dalek hybrids]]; Sec has a HeelFaceTurn after infusing himself with human DNA, leading to Dalek Caan overthrowing him.

* Series 4: Davros, despite being reduced to the "pet" of the new Supreme Dalek, directs his creations in stealing planets to construct the Reality Bomb and destroy all of existence. Caan is the GreaterScopeVillain who breached the time-lock surrounding the Time War to save Davros and rebuild the Dalek Empire, but he goes insane after witnessing the extent of his race's crimes and subsequently becomes their MadProphet to manipulate them into a situation where they can once more be destroyed.

* 2013 Specials ("[[Recap/DoctorWho50thASTheDayOfTheDoctor The Day of the Doctor]]" & "[[Recap/DoctorWho2013CSTheTimeOfTheDoctor The Time of the Doctor]]"): The Daleks were Gallifrey's primary enemies during the Time War, and are the most persistent of the alien races out to prevent the Time Lords' return by killing the Doctor before he can summon them. Additionally, Kovarian and her Silent Priests are retroactively revealed to have been part of a RenegadeSplinterFaction of the [[WellIntentionedExtremist Papal Mainframe]] that adopted a similar KnightTemplar stance on preventing a renewed Time War, only to unwittingly cause a StableTimeLoop that created the same cracks in the universe the Time Lords now threaten to return from in the process.

* Series 9: Rassilon is indirectly responsible for [[spoiler:Clara's death]] and imprisons the Doctor in the confession dial, ostensibly to force him to reveal the truth about the prophesized [[TheDreaded Hybrid]]. The Doctor [[BigBadWannabe easily deposes him]] after escaping, but temporarily becomes a VillainProtagonist when his own grief threatens the universe as he creates a massive paradox [[spoiler:to save Clara]]. The opening [[Recap/DoctorWhoS35E1TheMagiciansApprentice two]]-[[Recap/DoctorWhoS35E2TheWitchsFamiliar parter]] features a dying Davros as the ArcVillain tempting the Doctor into either committing genocide on the Daleks or providing them access to his regeneration energy, with Missy as a WildCard alternating between helping the Doctor and trying to kill Clara.

* Series 3: The "Harold Saxon" incarnation of the Master, after regaining his old memories, converts the remnants of humanity from a BadFuture into bloodthirsty Toclafanes before traveling to the present to get himself elected Prime Minister, proceeding to summon his forces from the future to first TakeOverTheWorld and then wage war on the entire universe. The Cult of Skaro also return for a [[Recap/DoctorWhoS29E4DaleksInManhattan two]]-[[Recap/DoctorWhoS29E5EvolutionOfTheDaleks parter]], experimenting with humans to create [[HalfHumanHybrid Dalek hybrids]]; Sec has a HeelFaceTurn after infusing himself with human DNA, leading to Dalek Caan overthrowing him.

* Series 4: Davros, despite being reduced to the "pet" of the new Supreme Dalek, directs his creations in stealing planets to construct the Reality Bomb and destroy all of existence. Caan was the one who breached the time-lock surrounding the Time War to save him and rebuild the Dalek Empire, but he goes insane after witnessing the extent of his race's crimes and subsequently becomes their MadProphet to manipulate them into a situation where they can once more be destroyed.

* Series 9: Rassilon is indirectly responsible for [[spoiler:Clara's death]] and imprisons the Doctor in the confession dial, ostensibly to force him to reveal the truth about the prophesized [[TheDreaded Hybrid]]. The Doctor [[BigBadWannabe easily deposes him]] after escaping, but temporarily becomes a VillainProtagonist when his own grief threatens the universe as he creates a massive paradox [[spoiler:to save Clara]]. The opening [[Recap/DoctorWhoS35E1TheMagiciansApprentice two]]-[[Recap/DoctorWhoS35E2TheWitchsFamiliar parter]] features a dying Davros tempting the Doctor into either committing genocide on the Daleks or providing them access to his regeneration energy, with Missy as a WildCard alternating between helping the Doctor and trying to kill Clara.

[[/folder]]

* Series 2: A BigBadEnsemble between the Cybus Cybermen and the Cult of Skaro. The former are Cybermen from a parallel universe who, after serving as the main antagonists of a [[Recap/DoctorWhoS28E5RiseOfTheCybermen two]]-[[Recap/DoctorWhoS28E6TheAgeOfSteel parter]], invade the Doctor's world in the finale. The latter are an elite group of Daleks, led by Dalek Sec, who opened the breach between the two worlds to release the millions of Daleks imprisoned in the Genesis Ark.

* Series 3: The "Harold Saxon" incarnation of the Master gets himself elected Prime Minister and summons a Toclafane invasion from the future so he can TakeOverTheWorld. The Cult of Skaro also return for a [[Recap/DoctorWhoS29E4DaleksInManhattan two]]-[[Recap/DoctorWhoS29E5EvolutionOfTheDaleks parter]], experimenting with humans to create [[HalfHumanHybrid Dalek hybrids]]; Sec has a HeelFaceTurn after infusing himself with human DNA, leading to Dalek Caan overthrowing him.

* Series 4: Davros, despite being reduced to the "pet" of the new Supreme Dalek, directs his creations in stealing planets in order to construct the Reality Bomb and destroy all of existence. Caan was the one who breached the time-lock surrounding the Time War to save him and rebuild the Dalek Empire, but went insane upon witnessing the extent of his race's crimes and subsequently manipulates them into being destroyed as their MadProphet.

* "[[Recap/DoctorWhoS30E17E18TheEndOfTime The End of Time]]": Lord President Rassilon is revealed as the GreaterScopeVillain behind the drumming that drove the Master insane as part of a gambit to escape his fate in the Time War. The Master himself is TheHeavy, resurrected by his cult and devouring humans to sate his hunger before turning everyone on Earth into clones of himself. Rassilon manipulates him into opening a portal to the time-locked Gallifrey, continuing his plan to destroy time and ascend the Time Lords to beings of pure consciousness.

* Series 5: The Silence are the [[GreaterScopeVillain Greater-Scope Villains]] who destroy the TARDIS in the future, consequently creating cracks in time that threaten to collapse reality. The closest thing to proper [[TheHeavy overarching antagonists]] in their absence is an [[LegionOfDoom Alliance]] of the Doctor's various enemy races, led by the New Paradigm Daleks, who blame him for the cracks and seal him in the Pandorica in the finale.

* Series 6: The Silence raise Melody Pond to assassinate the Doctor, believing that he will threaten the universe in the future. Madame Kovarian is TheHeavy as the leader of their faction and the one responsible for kidnapping Melody, but she's killed by the Silent Priests in the finale once she's [[YouHaveOutlivedYourUsefulness outlived her usefulness]].

* Series 7: The Great Intelligence is a being of pure thought that first comes to Earth in the form of living snow, mirroring the subconscious thoughts of a resentful, Victorian-era man named Simeon before evolving into a distinct entity. It sets out for revenge after the Doctor foils several of its schemes to take over the world, scattering itself throughout time in an attempt to undo all of the Doctor's victories.

* "[[Recap/DoctorWho50thASTheDayOfTheDoctor The Day of the Doctor]]" & "[[Recap/DoctorWho2013CSTheTimeOfTheDoctor The Time of the Doctor]]": The Daleks were Gallifrey's primary enemies during the Time War, and are the most persistent of the alien races out to prevent the Time Lords' return by killing the Doctor. Additionally, Kovarian is revealed to have been part of a RenegadeSplinterFaction of the [[WellIntentionedExtremist Papal Mainframe]] that adopted a similar KnightTemplar stance on preventing a renewed Time War (unwittingly creating the same cracks in the universe the Time Lords now threaten to return from in the process), while the [[VoluntaryShapeshifting Zygons]] are featured as the villains of the first special as they try to take over Earth.

* Series 8: The Mistress, or "Missy", incarnation of the Master collects deceased people from throughout history to resurrect as Cybermen. She uses them to disperse "cyberpollen" into the atmosphere and raise more Cybermen from graveyards across the globe, intending to slaughter and then upgrade the rest of humanity to create an army as a gift for the Doctor.

* Series 9: Rassilon is indirectly responsible for [[spoiler:Clara's death]] and imprisons the Doctor in the confession dial, ostensibly to force him to reveal the truth about the prophesized [[TheDreaded Hybrid]]. The Doctor [[BigBadWannabe easily deposes him]] after escaping, but temporarily becomes a VillainProtagonist when his own grief threatens the universe as he creates a massive paradox [[spoiler:to save Clara]]. The opening two-parter features a dying Davros tempting the Doctor into either committing genocide on the Daleks or providing them access to his regeneration energy, with Missy as a WildCard alternating between helping the Doctor and trying to kill Clara.

* Series 10: [[spoiler:The Saxon Master returns as TheHeavy, orchestrating the genesis of the Mondasian Cybermen to convert Bill, torture the Doctor, and stop Missy's HeelFaceTurn. However, the Doctor reprograms his Cybermen to include Time Lords in their definition of those who must be upgraded, forcing the Masters into an EnemyMine with him to escape the Cybermen's subsequent betrayal.]]

* Series 11: Tzim-Sha is a Stenza warrior and the Thirteenth Doctor's StarterVillain, 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 [[RealityWarper Ux]], stealing planets to power a superweapon he intends to use on Earth as revenge.

* Series 12: A BigBadEnsemble between the "Lone Cyberman" Ashad and [[spoiler:the "Spy" Master]]. The former tracks down the Cyberium to build a Death Particle and wipe out all organic life; the latter [[spoiler:massacres Gallifrey after learning the DarkSecret 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 BigBadEnsemble between the Sontarans and the two Ravagers, 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 [[AdvancingWallOfDoom Flux]]; the latter seek to destroy the universe and unravel the linear restraints of their master, [[AnthropomorphicPersonification Time itself]]. [[spoiler:Tecteun, the Doctor's adoptive mother and head of [[NebulousEvilOrganization Division]], is the GreaterScopeVillain who unleashed the Flux onto the universe after coming to view it as a failed experiment, but she's killed by the Ravagers when they hijack the Flux for their own omnicidal purposes.]]

* "[[Recap/DoctorWho2022CENThePowerOfTheDoctor The Power of the Doctor]]": The Master unites the Daleks and his [=CyberMasters=], led by a clone of Ashad, to wipe out humanity, while also planning to [[spoiler:capture his nemesis and force her through a regeneration so he can [[GrandTheftMe steal their body]] and commit atrocities in their name.]]

* Series 12: A BigBadEnsemble between the Lone Cyberman Ashad and [[spoiler:the "Spy" Master]]. The former tracks down the Cyberium to build a Death Particle and wipe out all organic life; the latter [[spoiler:massacres Gallifrey after learning the DarkSecret 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=]."]]

* "[[Recap/DoctorWho2022CENThePowerOfTheDoctor The Power of the Doctor]]": The Master unites the Daleks and his [=CyberMasters=], led by a clone of Ashad, to cause chaos as part of a gambit to [[spoiler:capture his nemesis and force her through a regeneration, intending to take their place and become the next Doctor.]]