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  • Ace Combat 7: Skies Unknown:
    • While he is technically on the player’s side, the main antagonist of the Spare Squadron arc is Colonel McKinsey, as he takes every opportunity to try to put the Spare Squadron down and hoard their accomplishments to himself in the hopes that he gets transferred over to a desk job.
    • Matias Torres is the main antagonist of the DLC missions, as Trigger and company are tasked with tracking him down after he goes rogue to carry out his ‘Ten Million Relief Plan’.
  • AMID EVIL has Boss-Only Level at the end of each chapter that houses a leader of each villainous faction:
    • Astral Equinox has Moon Guardian, a priest of the Astral Acolytes who seeks to bring pain to the worshippers of the sun from the same planet as his clan.
    • Domain of the Sentinels has The Scrounge, a source of the parasitic infection that has taken over the Sentinels.
    • The Sacred Path has Corrupt Spirit, a malevolent apparation who has awakened ancient guardians of the path and made them attack travellers to grow in power. He may or may not be the spirit of the Pilgrim.
    • The Solar Solstice has Solar Saint, a leader of Servants of the Sun who looks down on Astral Acolytes and trains his apprentices for future war.
    • The Forges has the Forgemaster, a Magitek robotic or cyborg inventor who created the many malevolent constructs seen throughout the dimension and seeks to constantly expand his army for conquest.
    • The Arcane Expanse sets up The Archmage of Chaos as the antagonist, but he turns out to have died long ago, leaving in his wake The Twin Terror, a duo of serpent-like creatures from beyond.
    • The Void has The Evil, a living personification of darkness, shadows and Void itself from age beyond ages. It is one way or another responsible for the corruption of every previous dimension, apparently doing it either For the Evulz or conquest and extending its power. All of this solidifies it's status as the Big Bad of the game.
  • Assassin's Creed usually has lower-ranking Templars as the driving force behind the events of smaller parts of the story and, of course, with an overarching Big Bad to each.
    • Assassin's Creed II: Francesco de Pazzi for the Florence arc, Jacopo de Pazzi for the Tuscany arc, and then Emilio and Marco Barbarigo family for the Venice arc. The Big Bad of the game is Rodrigo Borgia, who all the other Templars work for.
    • Assassin's Creed III: Edward Braddock for the prologue portion featuring Haytham, then William Johnson for the Boston Tea Party, John Pitcairn for Lexington, Concord, and Bunker Hill, Thomas Hickey for New York, and Benjamin Church for the missing supplies arc; Haytham is the Big Bad while Charles Lee is The Dragon. Nicholas Biddle serves as the Arc Villain for the naval missions.
  • Bendy and the Ink Machine has five chapters and multiple arcs to contain examples of arc villains:
  • Borderlands has Sledge as the main villain of the first quarter of the game. After being killed, Commandant Steele takes the role.
  • Bug Fables, as a Paper Mario-inspired game, naturally has one per chapter.
    • Chapter 1: The Spider is the guardian of the Artifact in Snakemouth Den who eats explorers.
    • Chapter 2: Venus, while not really a villain, is the antagonist of Chapter 2, as she holds the Artifact and makes the heroes brave her challenges.
    • Chapter 3: The Honey Factory Robots, which go haywire thanks to Code 32, guard the Artifact and try to attack the heroes and everyone else inside the factory, with Heavy Drone B-33 serving as the boss.
    • Chapter 4 has two of them:
      • The first half has Astotheles, the leader of the bandits who hold one of the keys needed to gain access to the Sand Castle and kidnaps Team Snakemouth when they infiltrate his hideout.
      • The second half has the Watcher, a roach who guards another artifact.
    • The secret Upper Snakemouth chapter has Zommoth, who killed the evil Roach Scientists experiemnting on bugs there and now haunts the lab.
    • Chapter 5: The Beast, a monster that guards the swamplands around the Wasp Kingdom.
    • Chapter 6: General Ultimax is the one in charge of Rubber Prison after taking it over.
  • Chrono Trigger has Lavos as the Big Bad, but being a story centered on Time Travel, each time period has a particular antagonist that takes up the role of the primary threat.
    • Prehistory (65 Million B.C.) has Azala, the psychic-powered queen of the Reptites who is waging war against the prehistoric humans led by Ayla.
    • The Dark Ages/Antiquity (12,000 B.C.) has Queen Zeal. She is the queen of the Kingdom of Zeal leading an effort to siphon Lavos's energy to make herself immortal, which eventually leads to her kingdom's demise. Uniquely among the Arc Villains, once she serves her purpose as an arc villain, she essentially becomes The Dragon to Lavos, staying by its side and enjoying her immortality.
    • The Middle Ages (600 A.D.) has the Fiendlord Magus. He is the leader of the fiends (mystics in the SNES version), magically-inclined monsters who aim to destroy the Kingdom of Guardia. He is also an Optional Party Member, as he was trying to destroy Lavos all along, and should the party spare him in his injured state during his second encounter, he joins the party, seeing them as his only chance at revenge, as he is actually Prince Janus of Zeal, whose kingdom was ruined by Lavos.
    • The Present (1000 A.D.) has the Evil Chancellor of Guardia. Once Crono and Lucca rescue Marle from the Middle Ages, the chancellor tries to get Crono executed for seemingly no reason, and later on, he deliberately escalates tensions between Marle and her father, the king of Guardia, and eventually tries to take over the kingdom by attempting to have the king himself executed. He turns out to be Yakra XIII, the descendant of one of Magus's fiends whose family has been plotting against the royal family of Guardia since the Middle Ages.
    • The Future (2300 A.D.) has Mother Brain, a supercomputer who was built to manage the robots and buildings in the future, but turned on humanity.
  • Deltarune:
    • Chapter 1: King sends his son Lancer and various other minions to stop the Delta Warriors from sealing the Dark Fountain so he could continue his quest to Take Over the World so that Darkners will rule supreme and Lightners will "live in despair".
    • Chapter 2:
  • Destiny has several major villains who menace the Guardians for a select expansion or quest line across the series.
    • Destiny (vanilla): The Sol Progeny emerge as the ultimate antagonists that the Guardians must defeat for the main campaign.
    • The Dark Below: Crota, a Hive warlord whose underlings are working to resurrect. After his death, he ends up paving the way for a much worse threat...
    • House of Wolves: Skolas, the self-proclaimed "Kell of Kells" who instigates an uprising against the Reef and seeks to unite the Fallen under his banner.
    • The Taken King: Oryx, the titular God-Emperor of the Hive and lord of the Taken who comes to avenge the death of Crota.
    • Rise of Iron: Aksis, Archon Prime of the House of Devils, is the one using SIVA against the Guardians for his own ends.
    • The Red War: Dominus Ghaul, the emperor of the Cabal's Red Legion who succeeds in capturing the Traveler and severing the Guardians from its Light.
    • Curse of Osiris: Panoptes is the one working against Osiris to implement a Bad Future where the Vex reign supreme.
    • Forsaken: Uldren Sov, brother of Mara Sov, masterminds a mass prison break of the Scorn and kills Cayde-6, which sets the player on their revenge quest.
  • Dragon Age
    • In Dragon Age: Origins, Keeper Zathrian is the Arc Villain of the Nature of the Beast quest and Uldred is the Arc Villain of the Broken Circle quest, though the other major quests track back to either Loghain or the Archdemon.
    • Dragon Age II had ones for each of its two primary DLCs. "Mark of the Assassin" had Duke Prosper de Montfort and "Legacy" had Corypheus who went on to become the main villain in Dragon Age: Inquisition.
    • Dragon Age: Inquisition: many quests feature their own self-contained villains: Gereon Alexius in "In Hushed Whispers", the Envy Demon in "Champions of the Just", Livius Erimond in "Here Lies the Abyss" and Duchess Florianne in "Wicked Eyes and Wicked Hearts". Areas that you explore also have their side antagonists with the Western Approach having Crassius Servis, the Exalted Plains having Gordian, the Emerald Graves having Knight-Captain Carrol and the Fallow Mire having the Hand of Korth. DLC campaigns also features the Avvar god of war and winter Hakkon in "Jaws of Hakkon" and the Qunari rogue agent Vissadala in "Trespasser".
  • EarthBound (1994)'s first four major towns are menaced by a major villain responsible for said town's woes and usually under the influence of Giygas.
    • Onett has Frank Fly, the leader of the Sharks gang who has a hold on the south side of the town and has the city in general in fear of them. After Ness defeats him, an impressed Frank befriends him and directs him to Giant's Step.
    • Twoson has Mr. Carpainter, a cult leader obsessed with the color blue and kidnapped second party member Paula to sway her to his side. It later turns out he was influenced by the Mani Mani Statue.
    • Threed has Master Belch, a slime monster terrorizing Threed with ghosts and zombies while enslaving the nearby Mr. Saturns to mass-produce his favorite food.
    • Fourside initially has corrupt mayor Geldegarde Monotoli seeming to be the area's major villain, but it turns out the true antagonist is the Mani Mani Statue, which has corrupted Monotoli and given him the ability to rule Fourside.
  • Fallout often has a single character acting as an antagonist in multiple quests in one area, disconnected from the main Big Bad.
    • Fallout: Decker, the most powerful crime lord of the Hub, the game's only real city. You spend multiple quests either working for him or working with The Sheriff to infiltrate his organization and take him down. This culminates in a shootout in his gang's headquarters.
    • Fallout 3: Allistair Tenpenny. He is widely known as one of the biggest troublemakers in the wasteland, and is the focus of three quests ("You Gotta Shoot 'Em In The Head", "Power of Atom", and "Tenpenny Tower"). You can also find other evidence of his villainy around the wastes, such as his former sex slave Mei Wong who just escaped, or a squad of roving mercenaries who have been hired by him to kill you for foiling his plans.
    • Fallout: New Vegas: Benny. Your characters spend the first third of the game tracking him down, dealing with the aftermath of his actions, and indirectly ruining his plans to take over New Vegas, all because he was the guy that shot you at the beginning of the game. Once his arc is over, the main story really starts to open up.
  • Final Fantasy XIV has a different main villain for each expansion and one for each raid series.
    • The original 1.0 version had Nael van Darnus or as later revealed in A Realm Reborn, his sister posing as him, who spearheads the Meteor project that causes Dalamud to fall. This lead to the Seventh Umbral Calamity, which capped off the game's disastrous and poorly-received first version in order to prepare for the relaunch.
    • A Realm Reborn has you facing off with Gaius Van Baelsar, another Garlean general who seeks to subdue the peoples of Eorzea for his empire.
      • The Binding Coil Of Bahamut Raid series has the titular dragonic Primal Bahamut as the main villain and final boss.
      • The Crystal Tower Raid has the Cloud Of Darkness, one of the most powerful Voidsent who desires to start an invasion of Eorzea.
    • Heavensward sets up Nidhogg, an extremely powerful dragon who holds an ancient vendetta against the Ishgardians. However, he ends up being slain as the Disc One Final boss; his role as main antagonist gets hijacked by the titular Heavensward themselves, lead by Archbishop Thordan VII. He uses Nidhogg's power to turn himself into a Primal version of Ishgard's old king, hoping to bring peace and order to their society through force. Nidhogg does return during The Stinger though, setting him up as a future threat, and indeed comes back as an arc villain for the first three main patches of Heavensward's post-launch cycle.
      • The Alexander Raid series has the goblin-led Illuminati and its leader Quickthinx Allthoughts as the force that desires to control the Humongous Mecha Alexander and its power to rewrite history in the hope to create an utopia for goblin-kind.
      • The Shadow of Mhach raid series has Diabolos, a powerful Voidsent who wants to resurrect Scathach the Shadow Queen.
    • Stormblood has you face off against Zenos yae Galvos, son of the Garlean emperor and Viceroy of the two nations you seek to liberate over the course of the expansion. Yotsuyu shares this role briefling during the Doma arc.
      • The Omega Raid series has Omega, a mechanical creature from an other planet with enough power to create digital pocket dimensions.
      • The Return to Ivalice raid series has Ultima the High Seraph, an ancient evil who is trying to escape from her prison by corrupting people with magical stones called auracite.
    • Shadowbringers doesn't initially have a face to its main antagonists, the Sin Eaters, though you are constantly hounded by the forces of the corrupt Lord Vauthry throughout the game. Turns out they are one in the same though, as Vauthry is in fact not only able to control the Sin Eaters; he is a Sin Eater, and the most powerful one in fact: the Lightwarden Innocence. However, like Heavensward before it, Vauthry is defeated before reaching the level cap and the main antagonist hat is taken by Emet-Selch — a.k.a. Solus zos Galvus, a.k.a. Hades — who serves as the final boss.
      • The Eden raid series has both Eden, the first Sin Eater which nearly destroyed the world a century ago with the Flood of Light, and a mysterious "faerie" which manipulates the amnesiac newcomer Gaia. Both villains are actually a single entity, the Ascian Mitron, who was mutated into a Sin Eater. His goals are to restore himself to his original form, force Gaia to remember her past life as his lover Loghrif, and create a utopia for the two of them at the expense of everyone else.
      • The YoRHa: Dark Apocalypse Crossover raid series has the Red Girl, the sinister artificial intelligence which governs the Machine Lifeforms.
    • Endwalker sets up a Big Bad Duumvirate of Fandaniel, a nihilistic Ascian who wants to bring about the Final Days, and Zenos again, back from the dead and thirsty for a rematch against the Warrior of Light. Fandaniel dies early on, but he still manages to set into motion the Final Days with his death, and with everyone, Warrior of Light included, more concerned about the Final Days, Zenos and his machinations quickly fade into the background. The heroes' search for the source of the Final Days eventually leads them to the actual arc villain, as well as Greater-Scope Villain, Meteion.
      • The post-Endwalker main story quests have Golbez, a Voidsent warlord who seeks to invade the Source using the power of the captive dragon Azdaja.
      • The Pandaemonium raid series has Athena, a rogue Ancient who orchestrated the nightmarish experiments taking place within the titular prison in a bid to make herself into a god.
      • The Myths of the Realm raid series has The Twelve, a pantheon of Jerkass Gods who want to Take Over the World now that Hydaelyn is out of the picture. In reality, they are benevolent gods putting up a Jerkass Façade, and their true goal is to test whether mankind is ready to live without their divine guidance.
  • Fire Emblem: Awakening: This game's plot can be divided into three story arcs, and each of these story arcs have a separarate protagonist and antagonist. In order:
    • Gangrel is the Big Bad of the first arc as he kills Emmeryn and declares war against Ylisse.
    • Walhart is the Big Bad of the second as he attempts to Take Over the World.
    • Grima is the Big Bad of the third, with Validar acting as The Heavy as he works to resurrect him. He qualifies as the Big Bad and not the Greater-Scope Villain because Grima travels back into the past in order to ensure his resurrection, not knowing that this would make his defeat possible. Confused yet?
  • Genshin Impact: While the Fatui and the Abyss Order are the overall main antagonists of the story, each chapter tends to have at least one villain that is responsible for the main conflict of the chapter.
    • Prologue: Dvalin (a.k.a. Stormterror) who the Abyss Order brainwashed into thinking that Humans Are Bastards, and Barbatos betrayed him.
    • Chapter 1: Tartaglia (a.k.a. Childe), as the Fatui sent him to Liyue to cause as much chaos as possible, and make him summon Osial. In actuality, all of Childe's antics were done so that La Signora can convince Zhongli to surrender his gnosis without Childe even knowing.
    • Chapter 2: The Raiden Shogun, who has been enforcing the Vision Hunt Degree in Inazuma, which ends up causing mass depression for everyone who lost their Visions. However, the Raiden Shogun's puppet turns out to be manipulated by the Fatui, making her an Unwitting Pawn for the Fatui's plans. She still serves as the final boss however, and the arc concludes with her Heel–Face Turn.
    • Chapter 3: The Akedemiya alongside Il Dottore and Scaramouche, as the former two wish to see the latter replacing Kusanali as the new Sumeru Archon.
    • Chapter 4: Marcel/Vacher serves as this for the two first acts of the Chapter, being responsible for Cowell's attempted murder on Liliane, the frame-up of Callas for the death of Jacques, and the serial disappearances of young women in Fontaine. After his death at the end of Act II, the All-Devouring Narwhal replaces him as the new Arc Villain, as it seeks to fulfill the prophecy that would wipe-out all of Fontaine.
  • With the exception of the second and third games who has Zeus as the main vilain, God of War has one villain each game and killed by Kratos at the same game.
  • A Hat in Time has Arc Villains for each chapter.
    • Chapter 1: Mafia Town has the Mafia of Cooks, who essentially kick off the plot by raiding Hat Kid's spaceship and causing her Time Pieces to be scattered around the world as a result. Their leader is the Mafia Boss.
    • Chapter 2: Battle of the Birds has either The Conductor or DJ Grooves, depending on who you choose to win the movie award. No matter who you chose, both attempt to use one of Hat Kid's Time Pieces in order to cheat and undo each other's movie award progress.
    • Chapter 3: Subcon Forest has The Snatcher; a shadow spirit who steals Hat Kid's soul and forces her to sign his contracts to do his dirty work. Later, when said contracts are complete, he then attempts to double-cross Hat Kid to claim all of the Time Pieces she has collected for himself. However, the Subcon time rift storybook reveals that Queen Vanessa is the Greater-Scope Villain responsible for The Snatcher's existence.
    • Chapter 4: Alpine Skyline has the Purple Flowers; a species of dangerous plants who corrupt the inhabitants of the level with their poisonous spores.
    • Chapter 5: Time's End has Mustache Girl who becomes the true Big Bad of the game once she steals all of Hat Kid's Time Pieces.
    • Chapter 6: Arctic Cruise of the Seal the Deal DLC is an inversion as it features No Antagonist whatsoever. Instead, the main conflict centers around Hat Kid accidentally crashing the ship into an iceberg and having to save all passengers and crew before it sinks.
    • Death Wish has The Snatcher return as the primary antagonist since Chapter 3, this time putting Hat Kid through Nintendo Hard contract challenges as Revenge for his humiliating defeat in said chapter.
    • Chapter 7: Nyakuza Metro of the Nyakuza Metro DLC has The Empress; a shady jeweler who is the leader of her own gang of crooks called The Nyakuza. She drafts Hat Kid into her gang upon realizing that she's after the same Time Pieces that her gang has a monopoly on, and once she discovers Hat Kid reclaiming her Time Pieces back, she calls a manhunt on her and nearly succeeds, only backing out once the police got involved.
  • The finale of the Henry Stickmin Series, Completing the Mission, gives you the ability to merge the endings of the two previous games into one. As a result, not every route can have the same villain.
    • All routes following Government Supported Private Investigator have Sven Svensson as the villain, who (unwillingly) became the Toppat Leader after the previous one was arrested alongside The Dragon.
    • Two of the three routes following Pure Blooded Thief have Reginald Copperbottom as the villain, remaining his status as the Toppat Leader due to never being arrested.
      • The one exception is merging this route with Convict Allies: The villain is now Dmitri Johannes Petrov, trying to recapture the heroes after the events of the previous game.
    • Three of the four routes following Relentless Bounty Hunter have the Right Hand Man Reborn as the villain, who took over leadership after Reginald was arrested.
      • The one exception is merging this route with Presumed Dead: The villain is Mr. Macbeth, the conductor of the Toppat Train, the main target of this route.
    • Two of the four routes following Rapidly Promoted Executive have Henry Stickmin himself as the villain. While no hero in the first place (most of the time), Henry becomes the Toppat Leader in those and might have a Jerk with a Heart of Gold streak depending on the player's choices. Meanwhile, General Galeforce becomes the Hero Antagonist, despite appearing in only one route.
      • One of the exceptions is merging it with Ghost Inmate: This time Ellie Rose becomes the villain, vengeful over being abandoned in the last game.
      • The other exception is merging it with The Betrayed: Reginald Copperbottom becomes the villain, being the one who killed Henry in the last game, making the vengeful Henry, now a cyborg, go after him.
  • In Infamous, each section of the city has its own antagonist. The Neon District has Sasha and the Reapers, the Warren has Alden Tate and the Dustmen and the Historic district is run by the Big Bad Kessler and the First Sons.
  • Kid Icarus: Uprising, with its gameplay divided into chapters, has several Arc Villains. Medusa for Chapters 1-9, Viridi for Chapters 11-14, The Aurum for Chapters 15-17, The Chaos Kin for Chapters 18-21, and Hades for Chapters 10, 22-25, and while he serves as the Big Bad for the whole game, he doesn't become a direct threat until those chapters.
  • The first saga of Kingdom Hearts, the "Dark Seeker Saga"note  has Master Xehanort, who is the cause of most of the problems the heroes face throughout the games through his various pawns and incarnations. For the Big Bad of each game of the saga:
    • In general, each Disney world visited in the games will feature the original Big Bad of the film the world is based on, attempting their original scheme or a variation of it which is stopped by the Keyblade wielders and the protagonist(s) of that film while the primary villain of the overall game continues their plan. This was more actively utilized in I, where the Disney villains were part of a Legion of Doom with Maleficent, and continued in a downplayed role with Maleficent and Pete interacting with each Disney villain in II. If it's not a Disney villain who is the major threat of a world, then a member of Organization XIII might cause the conflict. Or in the case of III, a Disney villain and an Organization XIII member may both be active in a world.
    • Kingdom Hearts at first seems to have Maleficent as the main antagonist, as she lead an alliance of Disney villains who control the Heartless, sought out the Princesses of Heart (several Disney princesses and Kairi) to open the Door to Darkness and access Kingdom Hearts, and corrupted Riku into opposing Sora. Only for her to turn out to be the Unwitting Pawn of "Ansem", the Seeker of Darkness (Xehanort's Heartless), who really controlled these Heartless and even possessed Riku.
    • Kingdom Hearts: Chain of Memories has Marluxia (Number XI of Organization XIII) for Sora's story, and "Ansem" for the Reverse/Rebirth storyline. The former leads the Organization members at Castle Oblivion and forces Namine to alter Sora's memories, with the goal of using him to overthrow Xemnas. The latter is the remnant of his presence in Riku, trying to retake control while Riku advances through Castle Oblivion and deals with the other Organization members.
    • Kingdom Hearts II has Xemnas (Xehanort's Nobody), founder and leader of the original Organization XIII, revealed to be using the hearts stolen by the Heartless to create his own Kingdom Hearts, and having previously recruited Sora's Nobody, Roxas, into the group (prior to Roxas defecting). At the same time, Maleficent has returned to life, aligned with the thuggish Pete, as they both try to acquire a new lair.
    • Kingdom Hearts coded has the data version of Sora's Heartless, the cause of the glitches. Things are complicated when Maleficent and Pete also hack in and manipulate events to their ends, and it's revealed after the defeats of "Ansem" and Xemnas, Xehanort has returned.
    • Kingdom Hearts: 358/2 Days has Saïx (Number VII of Organization XIII) as the closest thing the game has to a Big Bad, with Xemnas being the Greater-Scope Villain and the Heartless being The Usual Adversaries. Saïx assigns missions to Roxas and the other Organization members, but his cruelty is a wedge that stresses out Roxas' friendships with Axel and Xion (who Saïx especially dislikes), eventually driving Roxas to leave the Organization.
    • Kingdom Hearts: Birth by Sleep has Master Xehanort and Vanitas. Xehanort is shown in his prime and revealed to be an old Keyblade wielder whose actions drive the conflict of the series' later events. He splits the darkness from Ventus, which becomes Vanitas in the hopes of the two merging to create the X-blade and start a new Keyblade War (causing Ven to reside in Sora, with his likeness being used to create Roxas), manipulates Terra and eventually possess him (the resulting form of Xehanort becoming Ansem's apprentice and splitting off into "Ansem" and Xemnas), and it leads to Aqua being lost in the Realm of Darkness as a result.
    • Kingdom Hearts 3D [Dream Drop Distance] has a younger version of Master Xehanort, who time travels forward to aid "Ansem", Xemnas, and the old Xehanort in his true plan, to make a version of Organization XIII that contains various vessels controlled by Xehanort, then make them seek out seven lights to fight against, so the resulting battle between seven Guardians of Light and thirteen Seekers of Darkness can remake the X-blade. And Sora is targeted as one possible vessel when Young Xehanort interrupts Sora's and Riku's Mark of Mastery exams.
    • Kingdom Hearts III has Master Xehanort finally enact his master plan, now that he has his full Organization assembled, and the Guardians of Light ready, leading him to finally reforge the X-blade and start the Second Keyblade War he'd been pining for throughout the saga. The epilogue reveals that Braig/Xigbar, another apprentice of Ansem who had been working with Xehanort prior to him taking Terra's body, was the ancient Keyblade wielder Luxu, who also was the previous wielder of Xehanort's keyblade, in a new body as The Man in Front of the Man manipulating Xehanort for the Foretellers and the Master of Masters.
  • Kirby:
    • Kirby Super Star has this for each of its modes (the sole exception being The Great Cave Offensive, being the only mode which doesn't have a true Big Bad):
      • Spring Breeze, Gourmet Race, and Revenge of the King have King Dedede. In Spring Breeze, he steals all of the food in Dream Land just like in Kirby's Dream Land; in Gourmet Race, he challenges Kirby to a race to see who can eat the most food; in Revenge of the King, he seeks Revenge to finally defeat his Worthy Opponent once and for all.
      • Dyna Blade has the titular bird, who steals all of Dream Land's crops, prompting Kirby to stop her. It then turns out she did this so she could feed her chicks.
      • Meta Knight in Revenge of Meta Knight. His goal is to conquer Dream Land to end the lazy lifestyle of its denizens by unleashing his massive airship, the Halberd. He tries to stop Kirby by sending his Meta-Knights and some of the Halberd's strongest defenses at him.
      • Marx in Milky Way Wishes. He tricks the sun and moon into fighting, and sends Kirby on his mission to find all of the stars around the planets to summon the wish-granting comet Galactic Nova to stop this chaos. It isn't until Kirby summons Nova that Marx kicks him to the side, gets powers, and ultimately sets off the conquer Popstar.
    • The Dark Matter is this for the aptly named "Dark Matter Trilogy" (Kirby's Dream Land 2, Kirby's Dream Land 3, and Kirby 64: The Crystal Shards). Their main goal is to shroud the galaxy in darkness.
  • Knights of the Old Republic: Although Darth Malak is the overall Big Bad of the game, many of the locations the Player Character travels to have more immediate villains causing trouble.
    • Taris: Initially Brejik, the leader of the Black Vulkars, followed by Davik Kang, an Exchange crime boss.
    • Tatooine: The chieftan of a Sand People tribe responsible for attacks on Czerka Corporation's miners.
    • Kashyyyk: Chuundar, a Wookiee collaberating with Czerka Corporation to enslave his own people. The Player Character has a dark side option to side with him.
    • Manaan: The Sith Embassy for Ahto City, followed by the Progenitor for the Hrakert Rift.
    • Korriban: Uthar Wynn, the head of the Sith Academy.
    • Leviathan: Admiral Saul Karath, a Sith military officer who takes the main characters prisoner. After he is killed, Darth Malak arrives and becomes the Final Boss of the level
    • The Unknown World: The One, a Rakatan tribal leader who seeks to massacre a rival Rakatan tribe. After the Player Character defeats or helps him, they enter the Temple of the Ancients, where they are confronted by multiple Sith enemies until they reach the Temple's boss, a corrupted Bastila Shan, who has become Darth Malak's apprentice after being tortured by him.
    • The Star Forge: Darth Malak himself.
  • Knights of the Old Republic II: The Sith Lords:
    • Peragus Mining Facility arc: HK-50, followed by Darth Sion.
    • First Telos arc: Jana Lorso.
    • Dantooine arc: Azkul
    • Nar Shaddaa arc: Goto/G0-T0.
    • Onderon arc: General Vaklu
    • Korriban arc: Darth Sion.
    • Second Telos arc: Darth Nihilus.
    • Malachor V arc: Darth Traya, with Darth Sion Demoted to Dragon.
  • The Last of Us seems to have this in the form of a major threat persistent through each chapter, who is eventually faced as the boss near the end of it. You have, for each arc from start to finish: the dodgy arms dealer Robert from the Escape from Boston arc, the Bloater from the Bill's Town arc, the Looter's Humvee from the Pittsburgh arc, the cannibal hebephile David from the Winter Resort arc, and Marlene for the Jackson City arc.
  • Live A Live has the end boss of each story, which are all connected by a common thread that becomes clear in the game's final chapter:
    • Prehistory: "Odo", a Tyrannosaurus Rex worshipped by the Kuu tribe, to whom Beru is meant to be a sacrifice.
    • Imperial China: Ou Di Wan Lee, the leader of Indomitable Fist school that is trying to stamp out all possible rivals.
    • Twilight of Edo Japan: Ode Iou, a warlord who aims to rule over Japan by plunging it back into a bloody civil war.
    • Wild West: O. Dio, the leader of the Crazy Bunch, a gang of bandits terrorizing the town of Success.
    • Modern Day: Odie O'Bright, a martial artist aiming to establish his supremacy by killing every rival he faces.
    • Near Future: Odeo, an evil deity whose resurrection is key to The Conspiracy's plan to take over the world.
    • Distant Future: OD-10, the artificial intelligence of the starship Cogito Ergo Sum, which is planning to kill off the ship's entire crew.
  • Madagascar
    • Levels two and four feature an antagonist called the Zoohunter, who Marty has to beat to get outside the zoo, and the Penguins have to beat to take over the bridge.
    • Level nine introduces the albino crocodile, who Marty has to fight for one of the beacon pieces. He comes back with a vengeance in level ten, holding Mort hostage near the end of the level to race Marty down a waterslide.
  • While Mass Effect doesn't exactly have "Arcs" per se, it's worth noting that many of its side villains are standalone, found in single missions or 'campaigns' of missions, where a group of sidequests make up a single story. In the sequel, most of them are antagonists to a certain squadmate on a personal level, and so act as the main villain of that character's loyalty mission. Notable examples include Major Kyle, Helena Blake, and Lord Darius in the first game and Gatatog Uvenk, Weyrloc Guld, Tarak, Enyala, and Donovan Hock in the second game.
  • The post-game of Mega Man Star Force 2 has an actual storyline vaguely connected to the plot of the main game. It concerns MegaMan travelling to a possible Bad Future where Megaman didn't manage to defeat Le Mu. The cause of this future is Apollo Flame, who managed to Kill All Humans and subjugate all EM Beings.
  • While Octopath Traveler has a Big Bad and a Greater-Scope Villain in Lyblac and Galdera, respectively, the individual storylines of the game's eight main characters each have their own villain:
    • Ophilia's storyline has Mattias, the head of a cult for Galdera and the one behind the death of Ophilia's adoptive father and the corruption of her adoptive sister, all in a mission to steal the Sacred Flame and use it to weaken Galdera's prison and gain power from the dark god.
    • Cyrus' storyline:
      • Chapter 2 has Gideon, the scholar behind the kidnappings taking place in Quarrycrest, using the victims for his experiments to create blood crystals.
      • Cyrus' storyline overall has Lucia, who convinced Yvon, the headmaster of Cyrus' academy, to steal From the Far Reaches of Hell to help her start the blood crystal experiments, so as to allow her to become immortal in order to endlessly collect knowledge.
    • Tressa's storyline:
      • Chapter 2 has Morlock, the owner of the Quarrycrest mines, who underpays his workers and attempts to ruin Tressa and Ali's businesses by confiscating their skystones.
      • Chapter 4 has Esmerelda, a thief who steals Tressa's journal, and ultimately acts as the final opponent of her story.
    • Olberic's storyline:
      • Chapter 3 has the Lizardman Chiefs, the two leaders of a group of lizardmen currently attacking Wellspring.
      • Olberic's storyline overall has Werner, the man who orchestrated the fall of Olberic's home country by convincing his friend, Erhardt, to destroy it from within, and now acts as a ruthless tyrant over the town of Riverford.
    • Primrose's storyline has Simeon, the leader of the Obsidians, who killed Primrose's father for knowing about the Gate of Finis.
    • Alfyn's storyline:
    • Therion's storyline:
      • Chapter 2 has Orlick, a reclusive scholar living on the borders of Noblecourt who isolated himself from everyone after becoming obsessed with studying the Ruby Dragonstone, including Barham, his friend and former research partner.
      • Therion's storyline overall has Darius, Therion's former partner who backstabbed him and is currently after the Dragonstones that Therion himself is conveniently also after.
    • H'aanit's storyline has Redeye, a strange beast H'aanit's master was sent after, but she takes up the hunt after Redeye petrified her master, fighting it to find a way to save him.
  • Just like the original, Octopath Traveler II has a Big Bad and a Greater-Scope Villain in the names of Arcanette and Vide, respectively. And the individual storylines for the sequel's eight main characters each have their own villain:
    • Ochette's storyline has The Dark Hunter/Petrichor, the hunter responsible for Cateracta’s death, Tera’s sleep, Glacis’ isolation, exacerbating The Night of the Scarlet Moon and capturing the animal companion that Ochette didn’t choose and helped Harvey experiment on it, corrupting it into The Darkling that we knew from the beginning.
    • Castti's storyline has Trousseau, a former member of Eir’s Apothecaries who used to be kindhearted, softspoken man until one faithful day he came across a member of The Moonshade Order, who told him of the world’s dark, bloodstained history. Trousseau was immediately driven to insanity and came to view life as pointless suffering and seeks to bring the salvation of death for his Final Solution from his rain-spreading poison. It’s also revealed that the man behind the worst aspects of humanity that were used to teach Trousseau and drive him insane was a man named Claude.
    • Throné's storyline has Cluade, the true mastermind behind Throné’s journey to getting the keys to her freedom and is the founder of The Blacksnakes by impregnating countless women including Throné’s mother, and then he forces his countless children to kill each other just so only one of them has the strength to kill him so he can obtain his freedom. He’s also the man responsible for Trousseau's fall into madness by showing him the The Book of Night.
    • Osvald's storyline:
      • Chapter 1 has Warden Davids, the Warden from Frigit Isle who takes joy in overworking and beating the prisoners when they act out of line, and the obstacle that stands in the way of Osvald's plan to escape Frigit Isle.
      • Chapter 3 has Captain Stenvar, the corrupt captain of the guard in Conning Creek and the man who aided Harvey in framing Osvald for killing his wife and daughter. And he did this because… money.
      • Osvald's storyline overall has Professor Harvey, Osvald’s former scholar partner and the man who took everything from him by killing his wife and daughter and stealing his research for the One True Magic to take the credit. But as we continue the scholar’s story, we learn that Harvey actually bribed the judges to sentence Osvald to life-sentence instead of execution because he wanted to show off his research of the One True Magic to Osvald once he escapes Frigit Isle. And he didn’t kill his wife and daughter, but instead kidnapped and used them for his selfish experiments! Even worse, while Rita was killed and had her blood stored in Harvey’s Grieving Golem, Elena is brainwashed by him into thinking that he is her father so he can use her blood for Shadow magic! And what is the entire reason for this? Because he viewed Osvald as better than him!
    • Partitio's storyline:
      • Chapter 1 has Giff, the leader of a gang who keeps harassing Oresrush for years but was always driven away, until he suddenly gained power over the citizens. After his boss fight however, he begs Partitio to spare his life and tells him that he was working for Roque Brilliante, the actual mastermind behind the temporary downfall of Oresrush.
      • Chapter 2 and 3 have Thurston, Roque’s right-hand man who follows the establishment of the Roque Company. And he has Garnet take care of Partitio in the former chapter while also blaming him for Roque getting him fired from his job before taking on Partitio in the latter chapter. But just like Giff above, Partitio talks some sense into Thurston so he too can go through a Heel–Face Turn.
      • Partitio's storyline overall has Roque Brilliante, the landowner who sold the land to Partitio’s father but then he took it back once Oresrush was created and started bringing in money. Neither Partitio nor his father knew about Roque’s true intentions because the negotiations were done by post. But once Giff told the young merchant that the landowner is Mr. Roque himself, that’s when he decides to go on a journey to find him and get him to buy Oresrush back. And once again like Giff and Thurston beforehand after destroying the steam engine, Partitio manages to get Roque to come to his senses to make a Heel–Face Turn.
    • Agnea's storyline has Dolcinaea Luciel, a world-famous dancer while not remotely evil as the worst she does is attempting to tear down East Sai and renovate the district into her own image, is easily the closest thing to being Agnea’s primary and most recurring rival. And after defeating her in a dance, Agnea ends up befriending Dolcinaea and she even serves as one of Agnea’s hype women for her big show in the epilogue.
    • Temenos' storyline:
    • Hikari's storyline has General Mugen Ku, the samurai's older brother who is responsible for killing their father just so he can take the throne for himself and for ravaging the kingdom of Ku. This causes Hikari to journey the world to gain allies so he can be ready to stop him and bring back peace to the kingdom.
  • OFF is divided into different zones, and zones 1-3 have different guardians (Dedan, Japhet, and Enoch) that the player must eventually battle.
  • Ōkami has three major villains for the three main areas.
    • Orochi for the Kamiki Village arc.
    • Ninetails for the Ryoshima Coast arc.
    • Lechku and Nechku for the Kamui arc.
  • OMORI: Most areas in Headspace have one for each day, and they all serve to distract Sunny from the truth;
    • The Prologue has Captain Spaceboy, leader of a band of Space Pirates who refuses to help the heroes find Basil because he can't get over his breakup with Sweetheart.
    • Three Days Left has Sweetheart, the donut duchess who imprisons the characters in her dungeon after Hero rejects her advances.
    • Last Resort, the first half of Two Days Left, has Mr. Jawsum, who tricked everyone but Omori into signing contracts forcing them to work in his resort for the rest of their lives.
    • The bonus Orange Oasis area has the Unbread Twins, who created the monsters that roam the area.
    • The second half of Two Days Left has Hungry Humphrey and the Slime Girls, who are initially nice but attempt to kill the heroes to get at their clams.
    • The Faraway Town segments have the real world Aubrey, leader of the Hooligans who terrorize Sunny, Kel, and Basil.
  • Persona 5: The first several months of the game has you finding a series of new corrupt target for the heroes' Heel–Face Brainwashing. And while you eventually learn that The Conspiracy has been messing with the Metaverse as well, it's not until near the end that your team directly takes the fight to them.
  • While RuneScape has always had self-contained arcs dealing with quest chains, the game's overall lore came to the forefront in 2008 with the Wham Episode quest "While Guthix Sleeps," and since then a series of larger arcs incorporating details from many quest chains has been paramount. In order, the villains of these arcs have been:
  • Sam & Max: Freelance Police is a Telltale Game that has these types of villains in each episode within the three chapters:
    • Sam & Max Save the World has six episodes which deal with antagonists that have something to do with Mass Hypnosis as apart from their schemes:
      • Culture Shock has Brady Culture, washed out celebrity who uses his rivals The Soda Poppers to spread his brainwashing messages to the city.
      • Situation: Comedy has Myra Stump, a TV talk-show host, who has taken her audience captive.
      • The Mole, the Mob, and the Meatball has the Toy Mafia, lead by Don Ted E. Bear aka Harry Moleman.
      • Abe Lincoln Must Die! has Agent Chuckles and Abraham Lincoln, the former having been apart of the Toy Mafia to keep a tab on the brainwashing teddy bears, who then awakens Lincoln when Sam and Max destroy the brainwashing president puppet to ensure control of the U.S.
      • Reality 2.0 has The Internet itself, taking beta testers hostage in an MMO called Reality 2.0.
      • Bright Side of the Moon has Hugh Bliss, as well as being the mastermind of all of Season 1, being behind all the Mass Hypnosis schemes in order to hypnotize the world and feed on their bliss.
    • Sam & Max Beyond Time and Space has five episodes which deal with antagonists all being part of a conspiracy involving T.H.E.M., time travel, and hell.
      • Ice Station Santa has The Corporate Shambling Presence, a demon that was shipped to Santa and attacks the workshop.
      • Moai Better Blues has the spirit of Mr. Spatula, Sam and Max's pet goldfish, in a scheme involving an erupting volcano to signal T.H.E.M., destroy Easter Island, and get revenge on Sam and Max.
      • Night of the Raving Dead has Jurgen, a vampire that creates an army of zombies to collect their souls.
      • Chariots of the Dogs has Pedro, or T.H.E.M., a group of time and space faring mariachis that perform soul crushing with hell to pay for their space ship.
      • What's New, Beelzebub? has The Soda Poppers, who through the Power Of Hate, become demons and take over hell, having masterminded the second season to increase Hell's productivity and oust Satan.
    • Finally, Sam & Max: The Devil's Playhouse has five episodes that deal with antagonists who use the Devil’s Toybox in the scheme:
      • The Penal Zone has Skun-ka'pe, a Killer Space Monkey Evil Overlord who seeks the Toybox to conquer the world.
      • The Tomb of Sammun-Mak has Monsieur Anton Papierwaite, using Sameth and Maximus to get the Toybox and summon Yog-Soggoth.
      • They Stole Max's Brain has the evil ancient pharaoh Sammun-Mak himself, using the Toybox to rewrite reality and be its ruler.
      • Beyond The Alley of The Dolls has the Clone Master, aka Demonic Dummy Charlie Ho-Tep, one of the Toys of Power and specifically your ventriloquist ability, who wants to summon Junior and play with him at the expense of reality.
      • The City That Dares Not Sleep has the Narrator, also known as Max's never-used superego, using the memories of the Toys to keep Sam away until Max finally explodes and takes out himself, the Narrator, and half of the US as well.
  • Sly 3: Honor Among Thieves is the only game in the series where the various villains aren't working together under one Big Bad; the villain of each episode instead acts independently from one another. The antagonists as follows are Octavio in Episode 1, the Mask of Dark Earth for Episode 2, the Black Baron for Episode 3, General Tsao for Episode 4, Captain LeFwee for Episode 5, and Dr. M for Episode 6.
  • Super Mario Bros.:
    • Super Mario RPG: Legend of the Seven Stars has at least one major antagonist in each major section, which usually ends by collecting a Star Piece.
      • The Mushroom Kingdom arc has Mack, who holds the Light Blue Star Piece and invades the kingdom with his army of Shysters.
      • The Rose Town arc has Bowyer, who holds the Green Star Piece and is firing arrows into the town to paralyze the townspeople to make them into his living statues.
      • The Moleville arc has Punchinello, who is not a member of the Smithy Gang but is found guarding the Orange Star Piece and preventing the heroes from rescuing Dyna and Mite.
      • The Booster Tower arc has Booster, who is forcing Princess Peach to marry him, though he also isn't involved with the Smithy Gang, nor is he guarding the Purple Star Piece- that one is found after he is taken care of.
      • The Seaside Town arc has Jonathan Jones, a fearsome pirate who has claimed the Blue Star Piece as his treasure. Until Mario gets it back, after which the real arc villain turns out to be Yaridovich, a member of the Smithy Gang who sent Mario to claim the star for himself.
      • For most of the Nimbus Land arc, Queen Valentina, who usurped the throne of Nimbus Land from the real King and Queen, and must be defeated to find the true whereabouts of the Red Star Piece.
      • For the rest of the Nimbus Land arc, the Axem Rangers are out to nab the Red Star Piece from Mario, and end up needing to be fought as the arc's boss.
      • The Bowser's Castle arc has Exor, the giant sword who guards the way to Smithy's realm and is running the occupying forces of Bowser's Castle.
    • In Paper Mario 64, the boss of each chapter holds a Star Spirit captive.
      • The Prologue has the Goomba King, who blocks Mario's way to the rest of the game world.
      • Chapter 1: The Koopa Bros, who enslaved the Bob-Ombs in their fortress and holds Eldstar.
      • Chapter 2: Tutankoopa, who hides inside his tomb and holds Mamar.
      • Chapter 3: the "Invincible" Tubba Blubba, who is eating the Boos of the nearby village and must be beaten to find Skolar (as Bow will only give him up in exchange for beating Tubba Blubba).
      • Chapter 4: General Guy, who mastermind robberies in Toad Town and holds Muskular.
      • Chapter 5: Lava Piranha, who holds Misstar.
      • Chapter 6: Huff N. Puff, who is destroying Flower Fields and holds Klevar.
      • Chapter 7: The Crystal King, who holds Kalmar.
    • Paper Mario: The Thousand-Year Door:
      • Chapter 1: Hooktail terrorizes the citizen of Petalburg by eating them, holds the Diamond Star, and is holding Koops' father captive.
      • Chapter 2: Lord Crump, The Dragon to Sir Grodus, invades The Great Tree and oppresses the Punies to find the Emerald Star before Mario does.
      • Chapter 3: Rawk Hawk is the Champion of the Glitz Pit who holds the Gold Star in his belt and must be defeated for Mario to claim the Champion title and the star, except it's actually fake. Grubba, the boss of the Glitz Pit, is the real arc villain who is using the star to suck the youth out of fighters.
      • Chapter 4: Doopliss is a Duplighost who uses the Ruby Star to turn the citizens of Twilight Town into pigs and steals Mario's name and body.
      • Chapter 5: Cortez the ghost pirate holds the Sapphire Star as part of his treasure collection and sends his crew to stop Mario and allies from getting it.
      • Chapter 6: The Shadow Sirens do everything in their power to sabotage the Excess Express' voyage to Poshley Heights so they can beat Mario to the Garnet Star, and were originally behind the creation of the chapter boss, the Smorgs (though this was cut leaving them a Giant Space Flea from Nowhere).
      • Chapter 7: Lord Crump once again is the chapter villain, holding the Crystal Star on his base and waiting for Mario to find him.
    • Super Paper Mario:
      • Chapter 1 doesn't have a true arc villain, as O'Chunks only fights you briefly and Fracktail, the guardian of the Orange Pure Heart, only fights you when brainwashed by Dimentio.
      • Chapter 2 has Mimi, one of Count Bleck's minions who takes over Merlee's Mansion to steal the Yellow Pure Heart.
      • Chapter 3 has Francis the Chameleon, who kidnaps Tippi to make her a pet and post pictures of her. Defeating him grants Mario the Green Pure Heart.
      • Chapter 4 has Mr. L, who is sent by Count Bleck to beat Mario to the Blue Pure Heart in the Whoa Zone.
      • Chapter 5: King Croacus IV orders the enslavement of the Cragnons and holds the Indigo Pure Heart in his possession.
      • Chapter 6: Mimi and Mr. L show up to sabotage Mario's journey through the Duel of 100 to get the Violet Pure Heart.
      • Chapter 7: Bonechill, freed from his prison by Count Bleck, leads an invasion of the Overthere, and must be defeated for Mario to get the White Pure Heart.
    • Paper Mario: Sticker Star:
      • World 1: The Megasparkle Goomba holds the Red Royal Sticker atop the Goomba Fortress.
      • World 2: The Tower Power Pokey holds the Orange Royal Sticker in Drybake Stadium.
      • World 3: Gooper Blooper holds the Violet Royak Sticker in Whitecap Beach and is behind the pollution of the nearby forest.
      • World 4: Mizzter Blizzard holds the Blue Royal Sticker in Bowser's Snow Fort.
      • World 5: Petey Pirahna holds the Green Royal Sticker inside Rumble Volcano.
    • Paper Mario: The Origami King: Each member of the Legion of Stationary is the antagonist of the first five chapters, where it has captured a bunch of Toads and is guarding one of the streamers that need to be destroyed to get to King Olly.
      • Chapter 1: Jean-Pierre Colored Pencils the 12th guards the red streamer and has taken over the Overlook Tower, imprisoning its Toads.
      • Chapter 2: Rubber Band guards the blue streamer and is behind the invasion of Shogun Studios, where it keeps an audience of captive Toads to watch its performances.
      • Chapter 3: Hole Punch guards the yellow streamer and is the one who abducted the Toads from Shroom City to take them to the Temple of Shrooms, and is also the one who stole the sun.
      • Chapter 4: Tape guards the purple streamer and is holding a bunch of Toads captive in the Sea Tower.
      • Chapter 5: Scissors guards the green streamer and has taken over Bowser's Castle, where it is holding Bowser captive.
      • Chapter 6: Aside from King Olly himself, Stapler is the entity who Olly has been using to turn people into his Folded Soldiers and is guarding Olly's throne room.
  • While the Prototype is being set up as the Big Bad of Poppy Playtime, he doesn't appear for most of the time, letting other villains to rule over each chapter:
    • Chapter 1 has Huggy Wuggy, a somewhat brutish, but intelligent giant plush toy that stalks you throughout the facility after initial encounter.
    • Chapter 2 has Mommy Long Legs, a spider-like stretching plastic mascot who used to be a host of the Game Station, eager to "[1]" play with the Player Character. She sends several minions after the protagonist, such as Bunzo Bunny, the Mini-Huggies or PJ Pug-A-Pillar.
    • Chapter 3 has CatNap, a monstrous giant cat ruling over the Playcare facility capable of producing a hallucination and nightmare-inducing gas called the Red Smoke. The fanatical second-in-command and worshipper of the Prototype, CatNap stalks the protagonist throughout the chapter to taunt them while Miss Delight and the Mini-Smiling Critters are the characters actually trying to kill you.
  • Tales of Vesperia actually does this rather well:
  • The The Walking Dead (Telltale) video game has one every few episodes:
    • Season 1, Episode 2: The St. John family, with Andy as The Heavy.
    • Season 1, Episode 3: Ben, who is responsible for the entire conflict of the episode and only reveals his actions at the end. However, he's not a purposeful antagonist and remains part of the group for a while.
    • Season 1, Ep. 4 and 5: The Stranger, also the Final Boss of the season.
    • Season 2, Ep. 1 — 3: Bill Carver
    • Season 2, Ep. 5: Either Kenny or Jane, depending on the player's view of their rivalry.
    • Season 3, Ep. 1 — 3: Badger, albeit at Joan's behest.
    • Season 3, Ep. 4: Joan.
    • Season 3, Ep. 5: David Garcia in the second half.
    • Season 4, Ep. 1: Marlon with the Delta Raiders as the overarching threat of the season.
    • Season 4, Ep. 2 — 3: Lilly who doubles as the games Big Bad.
    • Season 4, Ep. 4: Minerva who tries to kill her brother Tenn and Clem's group after being bitten on the face by a Walker. Also serves as the Final Boss of the series.
  • Touhou Project: From Touhou Fuujinroku ~ Mountain of Faith until Touhou Kishinjou ~ Double Dealing Character, the goddesses of the Moriya Shrine were the driving force in the narrative. When something happened, it was either because of their schemes to gather faith, or the result of their faith gathering.
  • Undertale: The Ruins and the True Lab don't have one single antagonist threatening us throughout the area, though the same cannot be said for the game's remaining areas:
    • Snowdin: To stretch the limits of the word "villain", Papyrus constantly antagonizes the protagonist by sending out puzzles to solve, ending things with a fight at the end of Snowdin Town, with his older brother Sans constantly by his side. That said, both of them are completely friendly and goofy, with Sans specifically being chummy with the protagonist whenever Papyrus isn't around.
    • Waterfall: Undyne is the Captain of the Royal Guard who is dead set on murdering the protagonist to claim the final human soul needed to cross the Barrier; as Papyrus was ultimately just trying to impress her, she's also the Greater-Scope Villain of Snowdin. She is a silent, threatening Knight of Cerebus... until she takes off the helmet, revealing herself to be a gigantic Large Ham that is still dead-set on killing you.
    • Hotland and the CORE: Mettaton is an entertainment robot created by Dr. Alphys that, due to past programming that wasn't fully removed, wants to brutally murder the protagonist as part of his various TV shows, sending out mercenary-monsters to kill them when he's not doing it himself. Until it's revealed Mettaton has never gone "off-the-rails" at all: All of his encounters with the protagonist were staged so that Alphys could make herself look like a hero and convince the protagonist to stay in Hotland. Realising the protagonist is too weak to defeat Asgore, and that the king's genocidal intentions will definitely succeed if he doesn't step in, Mettaton actually goes off-the-rails by trying to steal the protagonist's soul for himself, saving humanity from extinction while becoming the greatest star of a whole new audience.
    • New Home: The game's Big Bad, King Asgore Dreemurr himself, the Underground's ruler who has been killing humans and stealing their souls for the sake of having enough to cross the Barrier seperating monsters from humand and exterminate the latter. Until you actually meet him in person, and it's revealed he is a sad, depressed, and frankly pathetic man who is deeply remorseful about everything he's done, but believes he has to keep the promise he made to his people all those years ago, stalling his fight with the protagonist for as long as he can. When you defeat Asgore, Flowey reveals himself to be the game's true Big Bad by stealing the human souls to become a god and show every creature alive "the true meaning of this world"; And this is all in the game's first ending, with the rest of Flowey's plans being revealed in the other endings.
  • Used fairly commonly in World of Warcraft. VanCleef is behind the low-level Defias arc, Naralex's Nightmare and the Crone of the Kraul are responsible for The Barrens' arcs, and following their father's (retconned out of continuity) death, the Big Bad Duumvirate of Onyxia and Nefarian are behind quite a lot of the rest of the plot.
  • Yu-Gi-Oh!:
    • Yu-Gi-Oh! Nightmare Troubadour is divided into three story arcs and has different main villains for each of them. The first arc has Para and Dox as minor antagonists with Bandit Keith and Pegasus being the boss fights. The second arc has you facing Noah, Gozaburo Kaiba, and the Big Five, while the third and last arc deals with Marik and Yami Marik.
    • Yu-Gi-Oh! Reshef of Destruction has Bandit Keith and the Neo Ghouls, who invade the town of Domino for a few chapters before moving back to the main threat, Pegasus and Reshef.

    Visual Novels 
  • Ace Attorney will generally have minor culprits to fill up your time until the last one or two cases, at which point the Big Bad will show up, though there are exceptions. The full list:
    • The first game has Frank Sahwit, Redd White, Dee Vasquez, and Damon Gant.
    • The second game has each case be completely standalone, so all of the villains (Richard Wellington, Mimi Miney, Acro, and Matt Engarde) are this, save for an accomplice (Morgan Fey) who shows up next game, as well as Shelley de Killer, who shows up in Investigations 2.
    • The third game has only Luke Atmey and Furio Tigre.
    • The fourth game has Alita Tiala and Daryan Crescend.
    • The fifth game has Ted Tonate, Florent L'Belle, and Aristotle Means for the core game and Marlon Rimes for the DLC case.
    • The sixth game has Pees'lubn Andistan'dhin, Roger Retinz and Geiru Toneido, plus Pierce Nichody in the DLC.
    • Investigations has Jacques Portsman, Cammy Meele, and Lance Amano.
    • Investigations 2 has Horace Knightley and Dane Gustavia. Surprisingly, no one else counts, as the other villains are all major players in the plot.
    • The Great Ace Attorney: Adventures has Jezaille Brett/Asa Shinn, Grimesby Roylott/Nikolina Pavlova, and Joan Garrideb (though the latter two never actually killed anyone, and their crimes were accidental).
    • The Great Ace Attorney 2: Resolve has Reiten Menimemo, Olive Green and William Shamspeare, and Enoch Drebbler and Dr. Courtney Sithe.
  • The Danganronpa games pit you against a series of murder culprits for the first four chapters before the final two have you fight the main antagonists.
    • Danganronpa: Trigger Happy Havoc:
      • Chapter 1: Sayaka Maizono attempted to murder Leon Kuwata, who fought back and killed her.
      • Chapter 2: Mondo Owada is the murderer of Chihiro Fujisaki.
      • Chapter 3: Celestia Ludenberg and her accomplice Hifumi Yamada are the culprits of the murder of Kiyotaka Ishimaru.
      • Chapter 4: Technically, Aoi Asahina is the antagonist of the chapter as she tries to get the other students killed for supposedly causing Sakura Ogami's death, though Sakura killed herself.
    • Danganronpa 2: Goodbye Despair:
      • Chapter 1: Teruteru Hanamura is the murderer of the Ultimate Imposter (though he was aiming for Nagito Komaeda).
      • Chapter 2: Peko Pekoyama killed Mahiru Koizumi.
      • Chapter 3: Mikan Tsumiki killed both Ibuki Mioda and Hiyoko Saionji.
      • Chapter 4: Gundham Tanaka killed Nekomaru Nidai in a battle to the death.
    • Danganronpa Another Episode: Ultra Despair Girls:
      • Chapter 1: "Hero" Masaru Daimon, leader of the Warriors of Hope, spends the chapter hunting down Komaru Naegi and Toko Fukawa.
      • Chapter 2: "Priest" Jataro Kemui lies atop Towa Tower and tries to stop Komaru from reaching the communications network.
      • Chapter 3: "Fighter" Kotoko Utsugi kidnaps Komaru, forcing Toko to save her.
      • Chapter 4: "Sage" Nagisa Shingetsu initally tries to help Komaru and Toko escape, but upon brainwashing by Monaca Towa, he instead tries to stop the girls from reaching the Big Bang Monokuma at the bottom of the underground base.
    • Danganronpa V3: Killing Harmony:
      • Chapter 1: Subverted - Kaede Akamatsu is supposedly the murderer, but she was framed by the mastermind, Tsumugi Shirogane.
      • Chapter 2: Kirumi Tojo is the murderer of Ryoma Hoshi.
      • Chapter 3: Korekiyo Shinguji killed both Angie Yonaga and Tenko Chabashira.
      • Chapter 4: Gonta Gokuhara killed Miu Iruma thanks to manipulation by Kokichi Oma.
  • The Spirit Hunter games have you face one of the titular spirits per chapter.
    • Spirit Hunter: Death Mark:
      • Chapter 1: Hanahiko haunts the first floor of H Elementary and kills any adult he sees with his Green Thumb powers.
      • Chapter 2: Shimi-O, real name Shinzou Maruo, is a fat spirit who haunts H Forest and drills holes in his victims to turn them into human beehives.
      • Chapter 3: For a certain definition of "villain", Hanayome, real name Seiko Hasegawa, calls people on payphones and helps them find lost objects, but tries to kill the heroes by ripping their eyes out when they claim to have seen "it" (the photos of her being raped).
      • Chapter 4: Miss Zoo, real name Manami Zukawa, haunts the second floor of H Elementary and is holding Madoka Hiroo prisoner.
      • Chapter 5: The Kannon Soldier haunts the Underground Shelter and kills anyone who wanders inside.
      • Chapter 6: Red Riding Hood, real name Sayako Shiina, haunts the abandoned Masquerade Love Hotel and kills anyone who steps inside.
    • Spirit Hunter: NG:
      • Prologue: Yuri Takamura haunts the underpass near Akira's home and is forced by Kakuya to try to kill him and Ami.
      • Chapter 1: The Urashima Woman, real name Himeko Shimizu, is the spirit haunting the Urashima Lake park and killing those who throw a rock in her lake.
      • Chapter 2: Kubitarou of Kintoki, real name Kaneko Ooishi, is the spirit terrorizing Kintoki by cutting off the heads of dogs.
      • Chapter 3: The Screaming Author, real name Tubasa Aoi, is the spirit haunting Miroku Manor who kills anyone that gets too close to the attic.
      • Chapter 4: Killer Peach, real name Tomoko Okayama, is the spirit haunting Moon Tower and killing the employees of the company working there.
      • Chapter 5: The Demon Tsukuyomi, who is an amalgamation of arsonist Masaru Ishimaru and his victims, must be summoned and defeated to win the penultimate round of Kakuya's game.
  • In Yumeutsutsu Re:Master, every route aside from Saki's has a villain that the hero must face :
    • In Kokoro's route, Ai and Kokoro who are inhabited by Nie and Majo must face The Real Ai Otori who actually lives in NieMajo's world when the latter tries to stop them to finish NieMajo and come back to their world.
    • Nana's route has two of them :
      • In Re:Master, there is Nana's abusive step-mother Mikage Nanamori who plans to have Nana come back to her in order to use her to make money.
      • In Re:After, The Editor has fallen in love with Nana. Thinking that Nana share the same though, she would stalk Nana in hope the latter accepts her feelings.
    • Marie's route has the anti-government group who plan to assasinate a high ranked of the governement and Marie's adoptive mother. Marie would infiltrate them to have them detroyed by the government.


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