Very common in Doctor Who, particularly during the Classic Series when it was comprised of multi-episode serials. Less so the Revival Series, which tended to have standalone episodes or two-parters, though it still had some season-long threats.
Classic Series
- Season 1:
- "An Unearthly Child": Kal the Caveman, the first in a long line of Doctor Who villains and the person responsible for its first two deaths before becoming the third.
- "The Daleks" has of course the Daleks, who would quickly become the Big Bads of the series as a whole.
- "Marco Polo": Tegana, who is responsible for the acts of sabotage against Marco's party, directing the bandits that harass them and attempting to assassinate the Khan. His master Noghai serves as the Greater-Scope Villain.
- "The Keys of Marinus": Yartek. He doesn't appear until the last episode but it is his actions that prompt the Doctor's party to go on their quest to find a way to defeat him.
- "The Aztecs": Tlotoxl, an Aztec high priest who plots against Barbara after she's mistaken for a goddess.
- "The Sensorites": The human Commander. His poisoning of the water supply has caused all the Sensorite deaths, leading to their hostility towards the new human ship and arguably to the City Administrator's Start of Darkness.
- "The Reign of Terror": Maximilien Robespierre, as the leader of the Revolution which causes all the Doctor and company's problems (at least until the end).
- Season 2:
- "Planet of Giants": Forester, a ruthless businessmen looking to launch a new insecticide harmful to life.
- "The Dalek Invasion of Earth": The black Supreme Dalek in charge of the Dalek-occupied Earth, with the referenced Dalek Supreme Command as the Greater Scope Villains.
- "The Rescue" two parter has Bennett, who set the whole Koquillion masquerade up to disguise acts of mass murder and genocide.
- "The Romans": Nero, who takes the Doctor and his companions captive shortly after their arrival in Rome.
- "The Web Planet": The Animus, a being seeking to envelop Planet Vortis in webs.
- "The Crusade": El Akir. Technically, he's a subject of Saladin, but after his failure to capture King Richard, his schemes are solely for his own gratification rather than for the sake of the Saracen cause.
- "The Space Museum": Governor Lobos, the leader of the Morok forces on Xeros.
- "The Chase": The black Supreme Dalek dispatching the assassination squad after the TARDIS crew.
- "The Time Meddler": The Meddling Monk, who plots to alter history so the English will "have jetlines by 1320."
- Season 3:
- "Galaxy 4": Maaga, leader of the war-like Drahvins.
- "Mission To The Unknown": The black Dalek heading the Dalek council and their plot.
- "The Myth Makers": As far as the Greek army the Doctor allies with are concerned, it's King Priam, although it's more a case of Grey-and-Gray Morality.
- "The Daleks' Master Plan": The Supreme Dalek in charge of the Dalek forces on Kembel.
- "The Massacre": Catherine de Medici.
- "The Ark": Monoid One, who plans to leave all the humans behind on the Ark and then destroy it with a bomb.
- "The Celestial Toymaker" has the titular Toymaker.
- "The Gunfighters": Pa Clanton is the head of the family and encourages his sons in their vendetta against Holliday and the Earps.
- "The Savages": Initially Jano. After his Heel–Face Turn, Captain Edal becomes the member of the Elders most determined to preserve the status quo.
- "The War-Machines": WOTAN, a power hungry and malevolent computer.
- Season 4:
- "The Smugglers": Captain Samuel Pike, the leader of the pirates.
- "The Tenth Planet": Gern, the Cyberman who takes over Geneva and is said to be in charge of their forces on Earth.
- "The Power of the Daleks": The Daleks. Various human schemers plot to use them to their advantage, but the Daleks eventually trump all of them.
- "The Highlanders": Grey, a crooked solicitor who is selling captured Highland clansmen into slavery in the West Indies.
- "The Underwater Menace": Professor Zaroff, a Generic Doomsday Villain who plans to drain the ocean into the Earth's core and thereby destroy the planet.
- "The Moonbase": The Cybermen, at it again.
- "The Macra Terror": The Macra, specifically the one known as Control.
- "The Faceless Ones": The Chameleon Director, who is co-ordinating the operation from their space station.
- "The Evil of the Daleks": The Dalek Emperor, who is also implicitly the Greater-Scope Villain for all the previous Dalek stories.
- Season 5:
- "The Tomb of the Cybermen": The Cyber-Controller, supreme leader of the Cybermen.
- "The Abominable Snowmen": The Great Intelligence, an intangible being trying to create a form for itself in order to take over the Earth.
- "The Ice Warriors": Varga, commander of the Ice Warriors plotting to take over Earth.
- "The Enemy of the World": Ramon Salamander, a Diabolical Mastermind plotting to take over the world.
- "The Web of Fear": The Great Intelligence again.
- "Fury From the Deep": The Weed Creature infesting the natural gas refinery.
- "The Wheel in Space": The Cyber-Planner, who directs the Cybermen on the Silver Carrier and the Wheel from their mother ship.
- Season 6:
- "The Dominators": Navigator Rago, the senior Dominator.
- "The Mind Robber": The Master Brain computer.
- "The Invasion": Tobias Vaughn, at least until the Cybermen well and truly prove to be Eviler than Thou.
- "The Krotons: The titular Krotons.
- "The Seed of Death": Slaar, the leader of the Ice Warriors who take over the moon.
- "The Space Pirates": Maurice Caven, leader of the titular pirates.
- "The War Games": The War Lord, leader of the evil aliens.
- Season 7:
- "Spearhead from Space": The Nestene Consciousness, with Channing acting as the face of its Autons.
- "Doctor Who and the Silurians": The Young Silurian. He is technically subordinate to the Old Silurian at first but has the virus intended to kill the humans released entirely on his own authority and, when he finds the Old Silurian has given the Doctor the means to find a cure, kills him and takes over.
- "The Ambassador of Death": General Carrington, who's behind the kidnappings of the ambassadors.
- "Inferno": Professor Stahlman. For the most part, he's an Unwitting Instigator of Doom, but his resorting to threats and sabotage so nothing stops "his" project are the cause of most of the problems in the story.
- Season 8: The Master acts as this for the season as a whole, although each story features him working with a different villain.
- "Terror of the Autons": The Nestene Consciousness again. The Master starts off working with it but later forms an Enemy Mine with the Doctor against it.
- "The Mind of Evil": The Master, taking center stage in this story arc with his plot to start World War III.
- "The Claws of Axos: Axos, who the Master starts off aligned with but eventually teams up with the Doctor against.
- "Colony in Space": Captain Dent, forming a Big Bad Ensemble with the Master.
- "The Daemons": The Master, who sets things off with his scheme to gain Azal's powers.
- Season 9:
- "Day of the Daleks": The gold Supreme Dalek, who's in charge of the Dalek forces on Earth.
- "The Curse of Peladon": A Big Bad Duumvirate of Arcturus and Hepesh.
- "The Sea Devils": The Chief Sea Devil and the Master, until the Sea Devils betray the Master and he allies with the Doctor against them.
- "The Mutants": The Marshal, who seeks to prevent Solos from becoming independent of Earth's Empire.
- "The Time Monster": The Master, who schemes to take control of Kronos.
- Season 10:
- "The Three Doctors" has the renegade Time Lord founder Omega.
- "Carnival of Monsters": Commissioner Kalik, the xenophobic Minoran bureaucrat with political ambitions who releases the Drashigs.
- "Frontier in Space": The Master, although it turns out that he's really being employed by the Daleks to start an interstellar war.
- "Planet of the Daleks": The Supreme Dalek in charge of the Dalek forces.
- "The Green Death": BOSS, a corporate supercomputer gone rogue.
- Season 11:
- "The Time Warrior": Sontaran Commander Linx
- "Invasion of the Dinosaurs": Charles Grover, head of Operation: Golden Age
- "Death to the Daleks": A Big Bad Ensemble between the Daleks and the City, with the Daleks even briefly forming an Enemy Mine with the Doctor.
- "The Monster of Peladon": A Big Bad Duumvirate between the Ice Warrior leader Azaxyr and Evil Chancellor Eckersley.
- "Planet of the Spiders": The Great One, ruler of the titular spiders.
- Season 12:
- "Robot": For most of the story, it's Hilda Winters, although the K1 Robot ends up being the Final Boss.
- "The Ark in Space": The Wirrn, with Noah functioning as the swarm leader until his Heel–Face Turn.
- "The Sontaran Experiment": Field Major Styre, with the Sontaran Marshal he reports to being the Greater-Scope Villain.
- "Genesis of the Daleks": Davros, creator of the Daleks and thus the main obstacle in the Doctor's mission to stop the creation of the Daleks.
- "Revenge of the Cybermen": The Cyber-Leader heading the Cybermen takeover of Nerva.
- Season 13:
- "Terror of the Zygons": Broton, Warlord of the Zygons.
- "Planet of Evil": The anti-matter creature.
- "Pyramids of Mars": Sutekh the Destroyer.
- "The Android Invasion": Styrrgon, the Kraal scientist who developed a lethal virus for their invasion.
- "The Brain of Morbius": Morbius, who seeks to have his brain implanted in the Doctor's body.
- "The Seeds of Doom": Harrison Chase, although by the last episode he's basically become The Dragon for the Krynoid.
- Season 14:
- "The Masque of Mandragora": The Mandragora Helix, who manipulates things to pave way for its emergence.
- "The Hand of Fear": Eldrad, a Kastrian criminal punished by disintegration but who survived as a spirit.
- "The Deadly Assassin": The Master, the mastermind behind the assassination.
- "The Face of Evil": Xoanon, who unusually ends up undergoing a Heel–Face Turn.
- "The Robots of Death": Taren Capel, the one reprogramming the robots to kill the humans.
- "The Talons of Weng-Chiang": Weng-Chiang, aka Magnus Greel, serves as the main antagonist of the story, leading Chang and the Tong of the Black Scorpion in their kidnapping of prostitutes to fuel his experiments with the Time Cabinet.
- Season 15:
- "Horror of Fang Rock": The Rutan, who masquerades as lighthouse-keeper Reuben.
- "The Invisible Enemy": The Nucleus of the Swarm.
- "Image of the Fendahl": The titular Fendahl, a prehistoric creature that feeds off life force.
- "The Sun Makers": The Collector, the Company's representative on Pluto.
- "Underworld": The Oracle, a haywire computer that rules over the survivors of the Minyan crew with the aid of the robotic Seers.
- "The Invasion of Time": Commander Stor, the head of the Sontaran forces and the one manipulating the Vardans as cover for the Sontaran invasion.
- Season 16:
- "The Ribos Operation": The psychopathic ex-dictator Graff Vynda-K.
- "The Pirate Planet": Initially, it seems to be the Captain, but it gets revealed in the second half to be Queen Xanxia.
- "The Stones of Blood": Cessair of Diplos, an intergalactic professional criminal.
- "The Androids of Tara": Count Grendel of Gracht, an aristocrat seeking to become King of Tara.
- "The Power of Kroll": A Big Bad Ensemble of Thawn and Ranquin, the former wanting to get rid of the Swampies and the other wanting to get rid of humans, and the titular Kroll itself.
- "The Armageddon Factor": The Black Guardian, although he spends much of the story acting through the Shadow.
- Season 17:
- "Destiny of the Daleks": Davros and the Daleks, in a Big Bad Ensemble with the Movellans.
- "City of Death": Scaroth, last of the warlike Jagaroth.
- "The Creature From the Pit": Adrasta, who throws the Doctor in the Pit when he refuses to work for her.
- "Nightmare of Eden": Tryst, ringleader of the drug smuggling operation.
- "The Horns of Nimon": The planet-devouring Nimon.
- "Shada": Skagra, who seeks to complete his brain jar and use it to control the universe.
- Season 18:
- "The Leisure Hive": The initial problems are caused by the West Lodge Foamasi, whose leader is posing as Brock, as they sabotage the Leisure Hive in the hope of buying it up. However, the hawkish Argolin Pangol becomes more and more of a threat as he plans to lead the Argolins back into war with an army of clones, ultimately serving as the Final Boss.
- "Meglos": The titular Meglos, who plans to use the Dodecahedron to power a superweapon capable of destroying entire planets.
- "Full Circle": The Marshmen, although they're mostly just acting on instinct.
- "State of Decay": The Great Vampire, a Sealed Evil in a Can whose release the Doctor is trying to prevent.
- "Warrior's Gate": Captain Rorvik, the head of a slave ship.
- "The Keeper of Traken": The Master, who orchestrated things to get himself a new body.
- "Logopolis": The Master. Although much of the destruction he causes is accidental and he ends up in an Enemy Mine with the Doctor for a while, he's quick to revert to his usual ways once he's in a position to do so.
- Season 19:
- "Castrovalva": The plot turns out to be yet another scheme of the Master.
- "Four to Doomsday": Monarch, an insane alien who believes himself god.
- "Kinda": The Mara, an evil entity that feeds off destruction.
- "The Visitation": The Terileptil Leader.
- "Black Orchid": George Cranleigh, the estranged son of Lady Cranleigh and perpetrator of the murders.
- "Earthshock": The Cyber-Leader in charge of the Cybermen invasion of Earth.
- "Time Flight": The Master, whose plot here is to obtain power for his TARDIS.
- Season 20:
- "Arc of Infinity": Omega, who is making another attempt to obtain a body for himself.
- "Snakedance": The Mara, which manages to reemerge and possess Tegan.
- "Mawdryn Undead": A Big Bad Ensemble between the Black Guardian, who is acting through Turlough, and Mawdryn.
- "Terminus": Another Big Bad Ensemble involving the Black Guardian, this time having him split it with Vanir leader Eirak.
- "Enlightenment": The Black Guardian, now taking center stage with his revenge plot.
- "The King's Demons": The Master, returning yet again to take another shot at the Doctor.
- Season 21:
- "Warriors of the Deep": A Big Bad Ensemble between the Silurian leader Ichtar and Senior Officer Nilson.
- "The Awakening": The Malus, an evil time-travelling alien war machine feeding on psychic energy.
- "Frontios": The Gravis their only articulate, thinking Tractator.
- "Resurrection of the Daleks": Davros and the Supreme Dalek, who both have their own agendas and end up clashing.
- "Planet of Fire": The Master, who's attempting another megalomaniacal plan.
- "The Caves of Androzani": Morgus, the story's most irredeemable and prominent villain, but notably he never actually meets the Doctor face-to-face.
- "The Twin Dilemma: Mestor.
- Season 22:
- "Attack of the Cybermen": The Cyber-Controller, who's returned to lead the Cybermen once more. The Cyber-Leader acts as The Dragon to him.
- "Vengeance on Varos": Sil, representative of the Galatron Mining Corporation.
- "The Mark of the Rani": A Big Bad Duumvirate between the Master and the Rani.
- "The Two Doctors": Chessene, an artificially evolved Androgum working with the Sontarans.
- "Timelash": The Borad, a mysterious dictator looking to provoke an interstellar war.
- "Revelation of the Daleks": Davros, the one orchestrating the eugenicist cannibalization of interred corpses at Tranquil Repose in order to use the best-quality bodies to create a new race of Daleks loyal to him while turning everyone else into food.
- Season 23: The Valeyard acts as the Big Bad for the season as a whole, though most serials focus on a different antagonist.
- "The Mysterious Planet": Drathro, ruler of the underground habitation.
- "Mindwarp": Kiv, leader of the Mentors.
- "Terror of the Vervoids": A three-way Big Bad Ensemble of Doland, Rudge and the Mogarians, and the Vervoids. Four-way if you include Bruchner, who ends up going nuts and trying to kill everyone.
- "The Ultimate Foe": The Valeyard, finally taking center stage.
- Season 24:
- "Time and the Rani: The returning Rani, who's been kidnapping the smartest people throughout space and time in order to create a gigantic artificial brain
- "Paradise Towers": Kroagnon, yet another Sealed Evil in a Can seeking to gain a new body.
- "Delta and the Bannerman": Gavrok, the leader of the titular Bannermen.
- "Dragonfire": Kane, a Humanoid Alien seeking the treasure of the dragon.
- Season 25:
- "Remembrance of the Daleks": A Big Bad Ensemble between the Dalek Emperor (really Davros), leader of the Imperial Daleks, and the Supreme Dalek, leading the Dalek Renegades against the Imperial Daleks in yet another Dalek Enemy Civil War.
- "The Happiness Patrol": Helen A, ruler of Terra Alpha and responsible for the enforced happiness on its population.
- "Silver Nemesis": A Big Bad Ensemble between the Cyber Leader, Lady Peinforte and Herr De Flores, all competing against the Doctor and each other to gain the Nemesis for nefarious purposes.
- "The Greatest Show in the Galaxy": The Gods of Ragnarok, whom the Circus of Fear exists to entertain.
- Season 26:
- "Battlefield": Morgaine, Battle Queen of the S'rax and Dominator of the Thirteen Worlds.
- "Ghost Light": Light. For much of the story, he's a Sealed Evil in a Can but becomes the Final Boss after the Doctor releases him in the hope he'll take care of Starter Villain Josiah Samuel Smith.
- "The Curse of Fenric": The titular Fenric, who turns out to have been the Big Bad of the Seventh Doctor's era as a whole.
- "Survival": The Master, returning to face the Doctor one last time for the Grand Finale of the classic series.
Revival Series
- The "Aliens of London"/"World War Three" two-parter in Series 1 has the Slitheen Family, chiefly Jocrassa Fel Fotch Pasameer Day Slitheen, the ringleader of their plan.
- Series 2:
- "Rise of the Cybermen"/"The Age of Steel" has John Lumic, creator of the alternate universe versions of the Cybermen.
- "The Impossible Planet"/"The Satan Pit" has the Beast
- Series 3: Mr. Saxon, aka the Master, the Doctor's most famous standalone antagonist.
- "Daleks in Manhattan"/"Evolution of the Daleks" has the Cult of Skaro, returning after their appearance in the Series 2 finale.
- "Human Nature"/"The Family of Blood" has the titular Family of Blood, who are hunting the Doctor.
- Series 4:
- "The Sontaran Stratagem"/"The Poison Sky" has General Staal, commander of the Sontaran invasion forces.
- "Silence in the Library"/"Forest of the Dead" has the Vashta Narada.
- Series 5:
- "The Time of Angels"/"Flesh and Stone" has the Weeping Angels.
- "The Hungry Earth"/"Cold Blood": Commander Restac, leader of the hostile Silurians.
- Series 6: "The Rebel Flesh"/"The Almost People" at first has Foreman Cleaves due to her dehumanizing treatment of the Gangers, but the role is eventually taken by Ganger Jennifer after she leads the Gangers in an uprising with the intent of waging war on the whole of humanity.
- Series 8: Missy, a.k.a. the Master's next, gender-bent incarnation, who for bonus points had a hand in the events of Series 7B by getting the Doctor together with Clara Oswald.
- Being more arc-based than other revival era seasons, Series 9 naturally has several.
- "The Magician's Apprentice"/"The Witch's Familiar" has Davros, who lures the Doctor to Skaro in a gambit to steal his regeneration energy.
- "Under The Lake"/"Before The Flood" has the Fisher King, the evil entity behind the hostile ghosts. Although by the present time the first part takes place, he's already been stopped by the Doctor traveling back in time in the second part, with the ghosts being after-effects from his plan.
- "The Zygon Invasion"/"The Zygon Inversion" has Bonnie the Zygon, leader of the Renegade Splinter Faction of Zygons looking to make war on the human race.
- Series 10: The "Extremis"/"The Pyramid at the End of the World"/"The Lie of the Land" three-parter has the Head Monk, leader of the Monk invaders.
- Series 11: Tzim-Sha ultimately serves as the main threat of the opener and closer, and his actions, mostly his part in Grace's death, provide the arc of the overall series.
- Series 12: The Master returns in a new form in the two-part series premier and finale, though more recurring throughout the season is Ashad, a.k.a. the Lone Cyberman.