Big Bad / Fan Works

Big Bad
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"The ultimate villain of the story, who's causing the problem the heroes must solve."

Note that Big Bad is not a catch-all trope for the biggest and ugliest villain of any given story. The Big Bad is the one who turns out to be behind several other seemingly independent threats.

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Ace Attorney

• Apollo Justice: Ace Attorney Case 5: Turnabout Substitution: Rhea Wits, the true identity of the Mysterious Bust Killer who Apollo spends the case trying to expose and bring to justice.
• The Dragon's Turnabout: The Honorable Judge is the real mastermind behind the Dragon Murders and the deaths of Ian Moriarty and Elliot Kane.
• Operation: Turnabout: Cpt. Adel Renard, who turns out to be behind almost every tragic event that occurs in the case and is the true murderer of Cpt. Janus Harvey.
• Phoenix Wright: Ace Attorney: The Contempt of Court: The leader of Aculeus, Hemlock. He's responsible for Renwick Smith becoming his puppet through blackmail and he's very heavily implied to be the one who killed Blaine Chill, which also implies that he also had a hand in the murder of Cedric Maplethorpe.
• Turnabout of Courage: Phoenix Wright, the true mastermind behind the deaths of Diego Armando, Larry Butz and Miles Edgeworth.

Adventure Time

• Alex (MovieVillain) has the titular antagonist herself from an Adventure Time fanfic. It turns out she's also the Man Behind the Man commanding the likes of Ice King, Ash, and Door Lord to do her bidding.
• Frozen Hearts (Red Witch): A Big Bad Ensemble between General Barton, who leads the surviving humans plot to take over Ooo, Sifine, the spirit of the crown trying to take over Simon's mind and return Ooo into a new Ice age, and Ash, who takes advantage of this commotion and leads the other wizards in taking over Ooo.

The Adventures of Tintin

• Wings Of The Fallen: Rastapopulus, who's reimagined as a demon who wants to end the world.

Animal Crossing

• The Terrible Secret of Animal Crossing: Penny is the one who's really running things. She has children sent to the island to be slowly turned into animals forced and forced to be subservient to her, lest she mutilates them and takes their body parts for herself.

Avatar: The Last Airbender / The Legend of Korra

• Avatar: The Last Airbender Revised has Zotu and Azul's father, Aizo, set up as the Big Bad in book one, with an expanded role in comparison to the original series' first season, but once Azul is properly introduced, it is clear that she will drive the plot far more-so than her father.
• In the Azula Trilogy, the overarching Big Bad is Zhan Zheng, the spirit of War, who has been manipulating Azun, Wei Ming, and Jian Chin in order to plunge the world into a perpetual state of chaos. Each of the three fics also has its own Big Bad:
  • Heart of Fire: General Azun, who wants to put Azula back on the throne and lead the Fire Nation in global conquest.
  • Path of Fire: Wei Ming, a girl with power over darkness who's out to make the rest of the world feel the pain that she's suffered.
  • Soul of Fire: Zhan Zheng finally takes center stage, possessing Jian Chin and granting him immense power.
• Played with in Kataang Island Adventure. Sharpclaw the raptor often attacks the islanders...but it turns out he does so to feed his isolated family. Once the situation calms down, Aang and Katara relocate him and his family to the mainland.
• Varium Fortune: Hiroshi hires Korra to find the man who broke into his house. However, it is eventually revealed that this is lie. He faked the break in to find the man who killed his wife and wipe out crime in the city. Hiroshi even has his daughter frame her for killing the man, and sends his daughter to build up an army to destroy the Triple Threats.

Barney & Friends

• Day of the Barney Trilogy: Unsurprisingly, Barney serves as the main villain, as the purpose of Jeremy and Fran's journey is to put an end to his reign over humanity.

Beastars

• Protector: Keiko, a black panther that goes also by Daisuke, is the most active and vindictive member of the ring distributing the bloodbone drug. While he doesn't start as the leader, he becomes one after Bill kills the previous leader.

Blood+

• Black Rose King: Alessandro Noirroi, a Chiropteran King bent on destroying Saya and Diva.
• Nobility: Didier is Prince Anjou’s brother who wants to kill him so he can become in line for king.

Cardcaptor Sakura

• Heart of Gold (Cardcaptor Sakura): Amatsu-Mikaboshi is the one driving the plot, seeking to destroy Amaterasu and shroud the world in eternal darkness.

Cross Ange

• Cross Ange: Futatsu Sekai no Border: Supreme Commander Alexia is the leader of the Reunion army, an organization of Norma who work for the True Earth and seek revenge on the now-powerless Mana people for their oppression; as such, she leads the Norma in attacking and persecuting the Mana people.

Crossover

• Ace Attorney | Zootopia Defence (Ace Attorney & Zootopia: Agent Jack Savage, the mastermind behind all the incidents you've been investigating.
• Avengers of the Multi-verse: The primary antagonists of the series is the Cabal, an alliance of the Avengers' greatest enemies that have come together to defeat them and conquer The Multiverse. It is led by a council composed of General Modula, Vlad Plasmius, Doctor Drakken, Vilgax, Van Kleiss, V.V. Argost, and the Dark Dragon.
• The Bagges Take Ostania (Courage the Cowardly Dog & Spy X Family): Jumping Jack Deen is the owner of a candy factory who is later revealed to be a robot created by the real villain of the fanfic Katz. After conspiring with a Westalian terrorist group, Katz distributes nanomachines in the candy. Upon activation, the citizens will become infected leading to them having to submit to Westalis by handing over their valuables.
• The Bridge (My Little Pony: Friendship Is Magic & Godzilla) has the mysterious entity that brings the Kaiju to Equestria, and creates a Legion of Doom out of the worst of them. It ultimately turns out to be Bagan. Letter developments reveal the Shadow King Grogar, the Nexus of Dark Magic and a being on par with Bagan and Harmony, also exists and is likely to share billing with Bagan for this trope.
  • The spinoff/side story The Bridge: Sound of Thunder has a Big Bad Duumvirate of the Mirror Universe versions of Godzilla and Cadence.
  • The spinoff crossover with The Shimmerverse, The Bridge: A Shimmer in the Dark, has Countess Mircalla, with Bagan acting as Greater-Scope Villain via his Aspect Mizu.
  • The Bridge: Humanity's Stand also has Bagan as Greater-Scope Villain, being The Man Behind the Man to the Red Dawn organization that serves as the primary antagonists.
  • Another spinoff Prequel, The Bridge: The Eclipse Times has Queen Chrysalis as the main villain during her original attack on Equestria a thousand years ago shortly after the banishment of Nightmare Moon.
• A Certain Magical Friendship (A Certain Magical Index and My Little Pony: Friendship Is Magic): In Context_SHIFT, Nightmare Moon, whose Eternal Night would cause The End of the World as We Know It by making the Earth too cold to live on.
• Child of the Storm (Marvel Cinematic Universe, Harry Potter, & others) has Lucius Malfoy as the spearhead of the first book's villainous alliance, with Chthon as a Greater-Scope Villain whose influence starts infecting Earth as an indirect result of Malfoy's actions and who serves as the book's Final Boss. However, it is made clear repeatedly that there are even more villainous factions at work in the shadows, waiting for the current conflict to resolve itself before any of them make their move.
  • Ghosts of the Past has something of a Big Bad Ensemble, due to being composed of a series of Story Arcs, each with its own villains, while Surtur is the Greater-Scope Villain acting as a looming bigger threat: The Forever Red arc has the Red Room led by General Lukin and Sinister; the Bloody Hell arc has Dracula in Harry's storyline and Voldemort and Selene in Dresden's; the Of Dungeons and Dragons arc has an Elder Wyrm; the Mirror Image arc has Dr. Robert Reynolds; and the Fallen Fortress arc has the spirit of the place.
  • The spinoff Unfinished Business has Nimue, who is trying to crack open Project Pegasus and use its heart to become the living embodiment of magic and Take Over the World.
• Chrono Reflect (My Little Pony & Chrono Cross/Chrono Trigger): has Lavos, as befitting a crossover. Though currently Lavos is acting as a Greater-Scope Villain, with Nightmare Moon as the Dragon-in-Chief.
• Coccinea (Kamen Rider Dragon Knight & Puella Magi Madoka Magica): Mayuri Kurotsuchi, who turns into Kamen Rider Abyss for the second phase of the final battle against him. He is responsible for the entirety of the events in the traitor game, using his Traitors as pawns to lure the rest of the inhabitants of the space station into being his guinea pigs. He's also Xaviax's last remaining commander that must be eliminated at all costs.
• Code Prime (Code Geass & Transformers): While the Autobot/Black Knight Alliance have several enemies throughouy the story in the form of Britannia and the Decepticons, namely Emperor Charles, it is ultimately Megatron that is the biggest threat. The Decepticon leader was responsible for Charles rising to power as Emperor by serving as Charles' mentor when the latter was a child, which meant Megatron is responsible for everything that happened under Charles's reign, including the invasion of Japan and other countries, as well as Lelouch and Nunnally's exile. Come Chapter 34 of R1, and Megatron asserts himself as such when the Decepticons invade and destroy Pendragon, with Megatron killing Charles.
• The Dark Lords Ascendant (Ranma ½ & Sailor Moon): Tanizaki Kazuo, a Corrupt Corporate Executive who has big plans to steal Sailor Moon's power, and plays a game of Xanatos Speed Chess to pit Ranma and the Nerima Wrecking Crew against the Senshi while he carries them out.
• Dragon Ball DC (Dragon Ball & DC Universe)
  • Vegeta during the Saiyan Saga. Like in canon, he leads the Saiyans attacking Earth. DARKSEID, the one who sent the Saiyans acts the Greater-Scope Villain.
  • Rogal Zaar and Comic Book/Sinestro for the Entity Saga. Rogal Zaar sees one of the view surviving Saiyans out in space and seeks to kill him. Sinestro starts off as Sealed Evil in a Can before manipulating the heroes into allowing his release. The two villains have apparently worked together in the past, and when Sinestro is free he attempts to help Rogal Zaar kill Kakarot.
  • The Super Saiyan Saga lacked a character in this role. Villains appeared but none that acted as a villain for the entire saga.
• Definitely Not Lupus (Once Upon a Time & House): The essence of the Dark One is behind Belle trapping House's team there, so that they can sacrifice Chase, Emma, and Regina to be free of Emma before it dies.
• Disney's RealmWalkers has "Him", the multiversal conqueror so feared that those who know of his existence do not dare speak his name. He is the Man Behind the Man to all the threats Sasha, Zami, and Heather have faced thus far, from the Illuminati to the demon that bursts out of the wall and attacks them (who Zami later explains to be a surviving version of Zhan Tiri, bound to "His" service by the deal she made with him to resurrect her.
• The Dragon and the Bow (Brave & How to Train Your Dragon): The Red Death, an giant intelligent dragon who destroyed the united Viking kingdom centuries ago.
• Eden's Diary (Future Diary & Assassin's Creed): John Bacchus, who in this universe is not only a Templar, but is also responsible for the tragedy that killed Yukiteru's uncle and Yuno's parents.
• Entities of Emotion (My Little Pony: Friendship Is Magic & Green Lantern) has a Big Bad Duumvirate of the Negative Entities (Parallax, Ophidian, and the Butcher), working together to conquer Equestria. By the climax, however, the Butcher has bonded with Nightmare Moon, with her taking the dominant role and his place in the alliance.
  • The sequel, Dark is the Night, has Black Lantern King Sombra, who is working to unleash the Blackest Night on Equestria.
• Equestrylvania (My Little Pony: Friendship Is Magic & Castlevania) has Dracula as its main antagonist. However, like certain games in the series (like Bloodlines and Portrait of Ruin), he's more of a Greater-Scope Villain (you know, due to being dead and everything), with the role of The Heavy falling to his minions (primarily Death and Actrise in this case) as they work to resurrect him.
• Equestria Girls: A Fairly Odd Friendship (Fairly OddParents & My Little Pony: Equestria Girls): initially sets up Mr. Crocker as the main antagonist, as he keeps enacting plots to try and expose Timmy's fairies. However, eventually the Dazzlings arrive on the scene and quickly usurp his spot, playing everyone else like fiddles as they work to corrupt Timmy and get his fairies' magic for themselves.
• Familiar Evil(The Familiar of Zero & Resident Evil): The Umbrella Corporation, being both the direct cause of the outbreak in the first place and creating many of the monsters that threaten the survivors in the city itself. They also sent U.S.S. Delta Team, or "Wolfpack", after Louise in an attempt to kidnap her for study.
• Fate of the Clans: Beast VI is the root cause of the Holy Grail War nearly breaking down, the creation of Cú Chulainn Alter, and the biggest present threat to humanity itself.
• Five Worlds War (One Piece, Bleach, Fairy Tail, & Naruto): Lord Konton, who kickstarted the war and recruited numerous villains from the four universes to create the Four Acts of Chaos to aid in his effort of world conquest.
• Game of Touhou (A Song of Ice and Fire & Touhou Project): First main villain is Mad Queen Eiki Shiki, responsible for plunging the realm in war due to her Knight Templar tendencies.
• Gaming All-Stars (Massive Multiplayer Crossover): The Ultimate Crossover has one between Dr. Eggman, G-Man, and Dr. Neo Cortext, though the latter doesn't have much influence on the plot until near the end. Remastered, on the other hand, changes the lineup to Eggman (Who has more screentime and more overall impact on the plot) and Colonel Mael Radec, who appears far less often in-series but is given more promotion by the series trailer and ultimately outlives Eggman, only being ousted by the Greater-Scope Villain once he thinks everything is going swimmingly for him.
  • In 2, there's Zinyak, who forms alliances with other aliens to form the largest threat seen in the series, and to a lesser extent, Shinnok, who only appears once but leads the forces of Netherrealm against the Earthlings on a scale almost as large as Zinyak's invasion.
• The God Empress of Ponykind (My Little Pony: Friendship Is Magic & Warhammer 40,000): The voice in Luna's head (later revealed to be Tzeentch), which corrupts her and causes her to turn into Nightmare Moon.
  • The sequel, The Warmistress of Equestria has Tirac as its Big Bad. Since he cannot yet manifest in the material world, his Dragon Scorpan is set up to be The Heavy until he arrives.
  • The second sequel, The Empress Returns, introduces the Dark God Ascendant, a powerful Chaos entity that killed the original four Gods of Chaos and wishes to see Celestia and the Imperium destroyed. Like Tirac above it cannot manifest in reality, so it has Lorgar and the Daemon Primarchs acting as its agents while it continues to grow in power.
• Halloween Unspectacular (Massive Multiplayer Crossover) is an anthology series, but each edition has a central Story Arc, with its own main villain. During most of the first Myth Arc (HU1 through HU4, specifically), this is a bit more fluid, as there are also individual arcs not connected to the larger arcs. By HU5, however, things are more settled, and definitely so by the second Myth Arc started in HU6.
  • In HU1, there's Witch Ember for her arc, and ReGenesis aka Dib for the main arc.
  • In HU2, there's the Underworld King for his arc, and Dan Phantom for the main arc.
  • In HU3, there's Dan for the Batavia arc, and Zombie King James I for the main arc.
  • In HU4, there's the Governor for the Gaol arc, and the alliance of Vlad, Morgan le Fay, Mr. Cromwell, and a mysterious cloaked figure for the main arc. That figure turns out to be the Governor as well.
  • In HU5, there's an alliance of all the previous major villains being manipulated by Sir Galahad.
  • HU6 and HU7 have General Rausseman of PURITY. HU8 continues the same Myth Arc, but establishes more of a Big Bad Ensemble: Rausseman is still there, albeit mostly behind the scenes, leaving the legwork to his lackey President Fulton. However, his actions have triggered the rise of two other forces determined to stop him at all costs — the Phoenix, who is willing to kill anyone even remotely connected to PURITY or Fulton's regime (even innocent voters), and Galactus, who is willing to destroy Earth to stop PURITY from using its resources to conquer the universe.
  • HU9 has the mysterious figure known only as the Stranger, who wants to destroy E350 as revenge for some prior offense. He's ultimately revealed to be the Bus Driver, the recurring joke character from the first five editions, who blames E350 for ruining his life. HU10 has him still in this role, as he prepares to finish crushing E350 and his friends for good.
• Harry Potter and the Mystic Force (Harry Potter & Power Rangers Mystic Force): Initially presents a Villain Team-Up of Voldemort and Imperious, but they're both pawns of the true mastermind, Ivan Ooze, who impersonated the resurrected Cedric Diggory and manipulated the wizarding world to turn against Harry as part of a larger plan to steal enough magic to Take Over the World.
• Help from afar (Avatar: The Last Airbender & Fullmetal Alchemist): Fire Lord Ozai masterminds the war, much like in the original show.
• Holy Diver (Danganronpa & JoJo's Bizarre Adventure): Dio Brando, who's running the Mutual Killing Game in a bid to destroy the last beacons of hope and have the world submit to him.
• Jaune Arc, Lord of Hunger (RWBY & Star Wars): Darth Nihilus, or rather his ghost, is the central antagonist of the fanfic. He's responsible for Jaune's gradual turn to the Dark Side and is plotting to take control of Jaune's body. However, Cinder Fall is still a major threat and she orchestrates several major events in her bid to destroy Beacon and steal the rest of the Fall Maiden's power.
• Justice League of Equestria (My Little Pony: Friendship Is Magic & DC Comics):
  • Mare of Steel: The first arc has General Zod, who attempts to eliminate Supermare as he plots to take over Equestria, while the second arc has a Villain Team-Up of Alexander Silversmith and Brainiac, who seek to destroy Supermare for their own respective agendas.
  • The Princess of Themyscira has Ares, who wants to unleash the hordes of Tartarus onto the world to create an endless war.
  • Darkseid is set up to be the Big Bad of the main Justice League Of Equestria story, being the Greater-Scope Villain of the series overall, who is responsible for an ancient war key to the backstory, and glimpsed in Mare of Steel as preparing for another invasion of Equestria.
• The J-WITCH Series (Jackie Chan Adventures & W.I.T.C.H.):
  • Season 1: Prince Phobos is the Evil Overlord of Meridian and primary antagonist of the Guardians and their friends, as per canon. Midway through the season, however, Tarakudo approaches him for a Villain Team-Up, working together to attain both Elyon's power and the Oni Masks in order for them to totally conquer both Meridian and Earth. Meanwhile, Cedric and Wong start plotting together to betray Phobos and take the Heart of Meridian for themselves, with each also scheming to betray the other to be the sole winner. And then in the final quarter of the season, Wong cuts a separate deal with Shendu to resurrect him with the Heart of Meridian in exchange for being told how to take all the Oni's power for himself. However, upon his rebirth, he betrays Wong to take all the power for himself, overpowering all the other villains and serving as the Final Boss.
  • Season 2: Also as per canon, Nerissa is the primary antagonist, though now with her son Drago acting as The Dragon. Together, they gather the Knights of Vengeance in order to strike at the Guardians and their allies as part of Nerissa's overall secret agenda.
• Kingdom Hearts: Cody's Story (Kingdom Hearts & Total Drama): Maleficent starts off as this at first, manipulating half the total Drama contestants to help her seek the hearts of all worlds. This is subverted in the Hollow Bastion chapter, where Ansem takes over as the villain for the rest of the story.
• Land of No Color (Digimon & Pokémon): Vendetta Rage, an extradimensional force inhabiting Princess Crystal's fiancée that has drained all of the color from the world.
• Lanterns of Equestria: Blackest Night (My Little Pony: Friendship Is Magic & Green Lantern) has the Black Lantern of Commander Hurricane as the primary antagonist, leading the Black Lantern invasion of Equestria, with the Black as the Greater-Scope Villain.
• The Legend of Banjo-Kazooie: The Jiggies of Time (Banjo-Kazooie & The Legend of Zelda: Ocarina of Time): Gruntilda hacks into the code of Ocarina of Time, allowing her to take over Hyrule and steal the Triforce, leaving Banjo and Kazooie to venture through the worlds and stop her.
• Magical Girls Unite Retransformed (Massive Multiplayer Crossover): Ichibey, the King of the Incubators, and the true mastermind behind the Law of Cycles.
• Max Wolf Revolutions (Massive Multiplayer Crossover): Dimonox/Abominox, an Eldritch Abomination who wants to destroy the entire Universe.
• Megami no Hanabira (A Kiss for the Petals & Shin Megami Tensei): Father Archibald Phillips, the leader of the Flock who caused the demon outbreak in Kazamino so his organization can stop it and look like heroes. When the situation gets out of control, he attempts to capture the Demon tamers to maintain his façade before deciding to destroy the entire city.
• My Little Avengers (The Mighty Thor & My Little Pony: Friendship Is Magic): Has Loki, who manages to manipulate the entire plot in his favor up until the Final Battle as part of his plot to Take Over the World.
• MLP Next Generation: Know Fear! (Green Lantern & My Little Pony: Friendship Is Magic): Has Stratus, The Emperor of the griffons, who starts the war with Equestria out of nothing but Fantastic Racism and a desire to Take Over the World.
• The Night Unfurls has Vault (in the original version), Eostia's greatest champion, as well as the leader of the biggest mercenary group in the land, known as the Black Dogs. His ambition to build a Sex Empire via Rape, Pillage, and Burn, hence starting a new war after the end of the Forever War, serves as the main driving force of conflict.
• One Piece: A Smash Adventure (One Piece & Super Smash Bros.): Most of the Big Bads the Straw Hats face are villains from their own respective series (Bowser in the Mario arc for example). But the Greater-Scope Villain instigating all of the events in the story turns out to be an organization of video game villains lead by Xemnas, until he's usurped by Dimentio.
  • Touhou: Journey to the Smashing Beyond also follows this same concept from the one above. This time, the organization is led by Tabuu, although Exdeath ends up being the True Final Boss.
• Persona Vein (Code Vein & Persona 5): Has Saklas, the Angel of Control that came from the alternate ending future of Persona 5 and literally has the alternate Yaldabaoth as his Persona. His plan was to challenge the Phantom Thieves in the main timeline that they defeated Yaldabaoth, and destroys their universe alongside himself so that society won't dictate their lives.
• Pokémon × Nimja: Play the Game (Pokémon & Nimja): HyPN0se, a Dutch-speaking Mewtwo whose ultimate plan is to wipe out not only all those who believe in the reality of hypnosis, but also the hypnotists themselves, in order to take over Amsterdam.
• Record Of Isekai (Massive Multiplayer Crossover): Being X, Black and Medea are the ones that convinced their fellow gods to destroy the mortals leading for the Ragnarok tournament to commence.
• Revival (Cthulhu Mythos & The Loud House):
  • The first fic has Maya Lottie an avatar of Nyarlathotep who stages the events of the story to usher in the entry of the Outer Gods.
  • The sequel King in Yellow has Hastur and Yog-Sothoth serving as a Big Bad Duumvirate. Hastur desires to take over the Earth by transforming humans into his Unspeakable Possessors and kill his half-brother Cthulhu, and Yog-Sothoth raises a reincarnated Cthulhu to use him as a weapon to kill Hastur and then have him start the apocalypse in his steed.
• Sonic the Hedgehog & My Hero Academia: The Hedgehog & The Deku (Sonic the Hedgehog & My Hero Academia): Eggman, Infinite, Stain, and later All For One, and Shigaraki are the main antagonists, teaming up to rid the world of All Might and Take Over the World.
• The Stars Will Aid Their Escape (Cthulhu Mythos & My Little Pony: Friendship Is Magic): Herald, who is implied, and eventually confirmed, to be an avatar of Nyarlathotep working to release the Outer Gods onto Equestria.
• In The Story to End All Stories, it's the one responsible for unleashing the Nothing. It turns out to be someone none of the characters had even heard of, let alone suspected.
• Super Mario Bros. Z (Super Mario Bros. & Sonic the Hedgehog): Turbo Mecha Sonic, renamed Metallix in the reboot, an upgraded Metal Sonic who turns against Eggman and destroys Mobius in an effort to gather the chaos emeralds so he may become the perfect being; continuing his rampage in the Mushroom Kingdom after Shadow transports the emeralds there.
• There Was Once an Avenger From Krypton (Massive Multiplayer Crossover): Several of the stories in this verse have their own main villain:
  • The Girl Who Could Knock Out the Hulk: Doctor Doom, who is pulling the strings of Project Centipede in their efforts to Take Over the World, seemingly as a means of preparing the Avengers to face a greater threat.
  • Changing of the Guard: Vilgax, who is responsible for all the attacks on Arcadia Oaks in search of the Omnitrix, which he wants in order to defeat Thanos at all costs.
  • To Rule Alone, To Build Together: Like in canon, Hawk Moth is responsible for all the Akuma attacks on Paris, in order to claim the Ladybug and Black Cat Miraculouses for his own ends.
• This Goddess Must Be Crazy (My Hero Academia & KonoSuba): Ainz Ooal Gown is the big bad of the series, having destroyed numerous worlds and seems to have no humanity left. Helping him is Tanya the Evil. Later on, upon seeing the My Hero Academia world is open, he plans on creating a Big Bad Ensemble, and using its strongest villains to destroy their own world, then continue on his multiversal rampage.
• Time Lords and Terror (My Little Pony: Friendship Is Magic & Doctor Who): Matron Hydia is The Heavy for most of the story, carrying out a plot to release the S'Muz and conquer The Multiverse... unfortunately for her, the S'Muz is an Omnicidal Maniac to the extreme, and it proves itself worse than Hydia by rendering her Deader than Dead before becoming the True Final Boss.
  • The sequel Mines of Dragon Mountain initially has Gabbro, who is willing to do anything to stop the Diamond Dogs from accidentally releasing Tirac. However, about halfway through, it turns out Tirac has been manipulating Gabbro the whole time, at which point Tirac becomes the direct Big Bad.
• Total Drama Infinite (Massive Multiplayer Crossover}: DIO and Cinder have formed an alliance to win the million. They're responsible for orchestrating several eliminations throughout the series and have forced others into their alliance only to eliminate them later.
• The Vampire of Steel (Buffy the Vampire Slayer & Supergirl) has John Vladislav in the first story, a boss of a vampire mob that intends to open a Hellmouth in Chicago and summon an Eldritch Abomination. The second story has Zol-Am, a Kryptonian turned vampire who assembles an army of vampires and demons to wipe out the Scooby Gang and Supergirl and then opening the Hellmouth.

The DCU

• But Doctor, I Am Pagliacci: Superman is this for the story and world at large. He leads the now malicious Justice League, practically controls the entire world, and is not only Lex Luthor, but is the reason why Batman doesn't exist anymore and the timeline is messed up.
• I Saw Grayson Kissing Santa Claus: For the entire story, Damian Wayne is convinced it's Santa. In reality, it's his older brother Jason Todd, who had the opportunity to correct Damian about Santa and instead egged his younger brother on for no other reason than screwing with the rest of their family.

Danganronpa

• Danganronpa Another: Utsuro, the mastermind behind the killing game and the true identity of Yuki Maeda.
  • Super Danganronpa Another 2: Mikasado Sannoji's Alter Ego, the Ultimate Wizard and the mastermind of the Utsuroshima Island Killing Game. He aims to resurrect Utsuro and steal his Divine Luck by forcing Yuki to relive his experiences through the killing game.

Danny Phantom

• The Collector: The titular Collector is the curator of a Ghost Zone Museum who captures Danny and Vlad to be apart of his exhibit, forcing the two to team-up in order to escape him.
• Silent Elegy's series of fan fics has a Big Bad Ensemble. Every story has its own Big Bad; in addition to the standalones, there are villains who are involved in multiple stories: Vlad, "Silver" Meryll Santiago, the Paranormal Society, and Technus takes center stage in several stories.

Digimon

• Digimon re:GENESIS: Era, a former DigiDestined who seeks to destroy the Digital World out of sheer hatred for Digimon.
• Digimon Trinity: The fic features a Big Bad Ensemble between Takeru and Hypnos, who are being pressured by the Japanese government to find a way to stop Digimon from bio-emerging in the Real World, no matter the cost; the Nightmare Soldiers, who are hoping to cultivate the partnership between Rika and Renamon as the first of several Tamers chosen to serve the Forces of Darkness; and Lucemon, who seeks to take the Digital Hazard from Guilmon and add it to his own to make himself stronger. And Zhuqiaomon and the Devas haven't even entered the picture yet.
• Tamers Forever Series:
  • BlackWargreymon fills this role in the second book Omni-Tamer by virtue of being the only recurring threat.
  • In Forget the Y2K, This is Madness!!, the sadistic Nightmare virus becomes the prominent threat to the Tamers,
  • However, the Nightmare itself pales when compared to the overwhelming power of the psychopathic Daemon, who sends his agent to weaken the Tamers during Theory of Chaos, before terrorizing them personally throughout Silent Sorrow.
  • Back in Card-O-Rama, Mr. Sagara comes across as this by attempting to rig the tournament, which Takato plots to counter for Rika's sake, but since this doesn't drastically affect the plot until the final chapter, most of Takato's interactions are with the judge/shop owner Sagara bribes, and both men are mere humans anyway, it's not nearly as memorable.

Disney Animated Canon & Disney

• Born to Be Wilde: The Count aka Count Reynard aka John Wilde is the Diabolical Mastermind who wants to take over all criminal organizations in Zootopia.
• C Ount Your Missing Sheep: Krampus, who has gone around kidnapping children from around the world, leaving Jack and the other holiday leaders to rescue them.
• Crowns of the Kingdom has Maleficent, who controls the Dispirations. The final fight with her comes after the one with Chernabog.
• Darkest Destiny: Cassandra, who after killing Zhan Tiri, obtains the Ultimate Power for herself; using it to take over Corona and force Rapunzel to be her wife.
• Disney's War — A Crossover Story: The Horned King, who manipulates various Disney villains into aiding him in destroying the multiverse and remake it in his own image. The sequels has the Master of the World (actually Alice), who kidnaps Alpha Beings and intends on using their magic essence to merge all worlds. However, it's revealed that the Horned King was controlling Alice the entire time.
• The Mulan AU fic Hachin has Bataar's half-brother Unegan as the main antagonist, though the ghoul in his service is the greater threat and turns out to be the one calling the shots.
• The Happiest Place: Maleficent, who leads the villains in their attempts to take over Disneyland for themselves.
• There are five of these in The Lion King Adventures:
  • Series One: Hago, a villainous lion with a magic cobra-shaped staff and aspirations to rule the world.
  • Series Two: Tama, who uses her powers of hypnosis as a desperate means of being loved.
  • Series Three: Death, who aims to rule the world, ending life as he pleases with his deadly touch.
  • Series Four: Shocker, a cub with electric powers who's obsessed with klling Simba and co., and The Vimelea, a race of alien parasites who invade and possess the residents of Pride Rock in an effort to take over the world.
  • Series Five: The Writer, the creator of the universe out to destroy all of creation. He's also the Greater-Scope Villain of the series, being responsible for every awful thing that Simba had to deal with.
• Hope for the Heartless: Arawn, the Death-Lord of Annuvin and the villain of the original books, is the Horned King's former master who was sealed inside the Black Cauldron centuries ago, and the reason that the Horned King committed all his atrocities that he is trying to atone for. He wants to have his former apprentice re-imprisoned with him so that he can continue torturing him forever; for that end, he's doing everything in his power to destroy his Redemption Quest and prevent Avalina from saving the Horned King's soul.
• Hope Springs Eternal: Hecate, a powerful, immortal witch and the self-proclaimed Queen of the Night, who plots to take over the Underworld.
• Opposites Destroy: Djinn, a Jackass Genie with a distain for humanity who wants to kill Genie for preventing him from harming their previous master.
• RJ: Reynard Junior, Nick Wilde's self-aware virtual avatar who intends to supplant the real Nick, kill Judy, and take over Nick's life.
• So Rot Vie Blut: Snow White, who has her father murdered and attempts to do the same to Grimhilde so she can have the throne for herself.
• Swear Not By The Moon: Zahn Tiri is the Evil Chancellor to Diadem who wants to provoke a war between Diadem and Corona and break up Rapunzel and Cassandra.
• Varian and the Seven Kingdoms: Donella, a mysterious woman who used to be friends with Ulla until she presumably killed her and now wishes to discover her secrets in search of power, and for now, that means employing Hugo to get close to Ulla's son, Varian.
• Wreck-It Ralph 2: [[spoiler:Princess Vanellope von Schweetz, Vanellope's evil Alternate Self and ruler of Sugar Rush II who wants to destroy the rest of the arcade games, including Sugar Rushh, so that hers can be the only one.
• The Wrath of Avelina: Avelina, who is putting curses on the Madrigals after blaming them for her curse.
• Zootopia 2 The Movie has Dr. Mouser, a Mad Scientist mouse and leader of a massive gang trying to take over the city.

Dragon Ball

• Dragon Ball Z Legacies: Over the course of the story, we are introduced to four major villains, each with their own independent goals: Varax, Sentinel, Kaiser, and Orthros. Varax is an alien warlord who wants to find Majin Buu so he can clone an immortal army to conquer the universe. Sentinel is a homicidal android created by Bulma when she first tried rebuilding Android 16. After going rogue, he goes into hiding with plans to kill the Z-Fighters and Take Over the World. He ultimately succeeds in the Bad Future that Pan and Eva came from. Kaiser Talos is an immortal supervillain who heads Capsule Corp's rival company and has secretly been creating Super Soldiers as part of a long-term plan to make Earth into a Galactic Superpower. However, all of them are overshadowed by Orthros (a.k.a. Alter-Videl), a nigh-omnipotent Dimensional Traveler determined to destroy every existing timeline and replace them with a single "perfect" reality built in her own image. Meanwhile, the threat of Esdraelon lurks in the background as the Gods do everything in their power to keep it from escaping its comet prison. At the end of the Phantom Enemy Arc, Orthros frees Esdraelon from its cell and sets its prison on a collision course for Earth.
• What If Frieza Turned Good?: Trogen, the Ax-Crazy third son of King Cold and his intended successor after exiling Frieza. Initially, King Cold's exile of Frieza and creation of Trogen causes the conflict, but he ends up dead by Trogen's hand as his drive to kill Frieza surpasses Cold's desire to leave a successor to run the empire. From there, Trogen is regarded as the biggest threat in the story.

The Elder Scrolls

• Endreal: The High Ones, a race of evil godlike entities who intend on starting the Cleansing; an event that would destroy all of humanity.
• Falskaar: Yngvarr, the Jarl of Staalgarde, fills this role for most of the quests on the island, as most of the bad events that happen are his responsibility in some way; on top of that, many of the bandits in Falskaar work for him in some capacity. His ultimate goal is to steal the Heart of the Gods and become immortal.
• The Forgotten City: The Arbiter and Jarl Metellus. The Arbiter is the Dwemer who has been enforcing the Draconian laws of the city while Metellus is violating the law in secret to rape Maisi nightly.

The Fairly OddParents!

• Burning Black at first seems to have Remy as its central antagonist, but it eventually turns out that he's working with the Pixies, who seem to be using him as a means to fulfilling their own agenda.

Fifty Shades of Grey

• Poor Unfortunate Souls: Christian Grey himself is Ana's abusive boyfriend who had previously ruined the lives of about a dozen girls prior, and the two detectives, Lindsey and Ailea, have the job of saving Ana and apprehending Christian.

Five Nights at Freddy's

• Five Nights At Freddy's: Lost Souls: The theme park is regularly haunted by a malevolent entity at midnight. It's incredibly aggressive and capable of trapping anyone still in the park at that time in an all-encompassing fog, preventing them from escaping.

Fullmetal Alchemist

• Asylum (FMA): Dante is the main antagonist, siphoning power from alchemically gifted patients and switching bodies with female ones to prolong her own life.

Fusion Fic

• Danganronpa: In Harmony's Wake: Monoponi is the one who trapped the character on the cruise ship and forced them to participate in the Killing Game. As it turns out, his true identity is Cozy Glow, who was freed from her stone prison and ended up in the human world. She started the Killing Game as a means of getting Twilight to come to the human world and drive her to despair, so she may drain her of her magic and use it for herself.
• Death Note Equestria: As Villain Protagonist, the role falls to Twilight by default, using the Death Note to pass judgement on those she believes are criminals in an effort to make Equestria a better place. Though one could argue that Mer takes on the role of The Heavy (if not outright Big Bad) during Twilight's Memory Gambit, even though everything is going according to Twilight's plan.
• Empathy has a Villain Team-Up between Yokai and Captain Smek, working together to open a portal for the latter's master, the Gorg.
  • The sequel Unity has the shadowy figure called Enigma. What he wants isn't known yet, but he appears to be plotting against the world's heroes.
• A Storm of Chaos: A Doctor Whooves Adventure: At first it looks like The Master is the main villain, but it quickly turns out he's an Unwitting Pawn of Borusa, who's using him to distract the Doctor from his own plans.

Godzilla

• Abraxas (Hrodvitnon): Ghidorah, which is directly or indirectly responsible for all the two protagonists' (San and Vivienne Graham's) pain and suffering since before the fic's start. Taking over from Alan Jonah as the true main threat, Ghidorah telepathically commands the Many and deploys them against the heroes, seeking to take Vivienne back so it can torture her into irrevocable insanity (without caring what happens to San), before it resumes its plans to kill off humanity and all life on Earth.
• NES Godzilla Creepypasta: Red, the entity haunting Zach's playthrough, and the culprit behind the death of Melissa, his former girlfriend.

Harry Potter

• In Dumbledore's Army and the Year of Darkness, as in the books, ultimately, Voldemort. Memories of the horror of his reign and the extremes required to end it echo through the sequels.
• Harry Potter and the Methods of Rationality: It seems like either Dumbledore or Voldemort is this depending on political orientation. The real Big Bad is Quirrell/Voldemort, who causes most of the problems in the story, although he's actively trying to help the heroes save the world from Harry for entirely selfish reasons.
• My Immortal: In theory, Voldemort is the main antagonist and the story attempts to present him as such, but he's a Harmless Villain who doesn't actually do anything except show up, yell at Enoby, then leave.

Henry Stickmin Series

• Begrudging Assistance Requests: While he's given a bit of Adaptational Heroism, Dmitri Johannes Petrov, The Warden of The Wall, still opposes protagonist Ellie Rose (who in turn is given some Adaptational Villainy), making him the Hero Antagonist to her Villain Protagonist.

High School D×D

• Marriage of Heaven and Hell: Halja, the Norse Goddess of Death and the current ruler of Heaven. She's the main threat that the ORC seeks to take down and is in charge of the villains that they face.

The Hunger Games

• Saving the Boy: Original Character Misu Teeyer, who is the one to replace Katniss as the female tribute for the Seventy-Fourth Hunger Games^note Katniss was reaped for and won the Seventy-First Hunger Games instead in the backstory. While Snow is still the Greater-Scope Villain, Misu drives most of the conflict of the story due to her hatred of Katniss and desire to win the Games. She is the biggest threat to Peeta in the arena, and makes it all too clear she intends to kill him, not just for the sake of survival but also to spite their female mentor.

Invader Zim

• Becoming a True Invader has the mysterious figure known as the Employer, who is leading an army in conquering the Irken Empire as a prelude to taking over the whole universe. He eventually turns out to be Minimoose, of all characters, who is actually a Control Brain from an Alternate Universe.
• For the Glory of Irk: The Control Brains are the Big Bad Duumvirate behind The Conspiracy driving the plot, with IX (the Control Brain on the Massive) acting as The Heavy and primary leader. They are brainwashing Irkens to turn them into agents that will further events to cause a war with the Syndicate. They're doing this so that the Tallest will trigger the War Protocol, which will enable them to turn all Irkens into a Hive Mind that they can control, feeling that they're the only ones who can properly rule the Empire.
• Invader Zim: The Universe Killer has Venagile the Grinning Demon, an Eldritch Abomination who takes sadistic pleasure in slowly destroying dimensions one world at a time, and who has now set his sights on Earth.
• My Hostage, Not Yours:
  • My Hostage, Not Yours: The Valkian Queen, who's trying to steal the LEECHY from Gaz so she can defeat the Irkens.
  • The Revenge of Player 2: Iggins, who wants revenge against Gaz for past actions against him.
  • The Inevitable Takeover: Zim and Gaz, who switch from Anti-Heroes/Anti-Villains to full Villain Protagonists to take over Earth. The Tallest could also be seen as the Greater Scope Villains, since Zim is still loyal to them.
  • Re: My Hostage, Not Yours: Like the original story, this version has the Valkian Queen, who is now a Hive Queen of a race of Bee People (instead of a Lizard Folk monarch). It's his attempt to flee the Queen that leads to Larb crashing onto Earth and his PAK ending up on Gaz, and the climax is kicked off when her minions hunt Gaz down to retrieve the PAK and the encrypted data hidden on it.

Jackie Chan Adventures

• Jackie Chan Adventures: Olympian Journey has Eris, the Goddess of Discord, who wishes to gather the essences of the other slain members of the Greek pantheon in order to restore the dominance of the gods over humanity.
• Queen of All Oni has Jade, who upon being transformed back into the Queen of the Shadowkhan, dedicates herself to being the greatest and most successful villain her family has ever faced, with the entire plot being built around the other members of the Chan Clan trying to stop her schemes and find a way to return her to normal. Meanwhile, Tarakudo is the Greater-Scope Villain trying to manipulate events remotely so that he can get free and Take Over the World. When he's successfully freed during the Final Battle, he and Jade come to blows over leadership of the Shadowkhan, with Tarakudo ultimately winning and serving as the Final Boss.
• Shadows Awakening has a somewhat complex Big Bad Ensemble: Daolon Wong is definitely The Heavy, being the one who instigated and drives the plot, but partway through the story he allies with The Phantom/Kyosuke, who makes it clear from day one that he's only using Wong to further his own ends. Meanwhile, in addition to the heroes, they're also at odds with another Villain Team-Up of Tarakudo and The Queen (who seems to be chafing under Tarakudo's leadership), who want to corrupt Jade for their own purposes.
  • This setup is resolved near the end of the story — Wong is defeated by the heroes, but the Queen's corruption of Jade is completed enough that the Tiger Talisman responds by separating them, giving the Queen a body of her own to work with; she defeats the heroes and depowers Wong, at which point Kyosuke reveals he and the Queen cut a deal behind their partners' backs, and now that she's proven herself worthy, he declares loyalty to her, demoting himself to her Dragon. So, in the end, it appears that the Queen has emerged from the Ensemble as main antagonist.

Kirby

• Kirby: Right Back at Ya! Odyssey of Dreams: Overlord Zero, the ruler and creator of Dark Matter, who's trying to invade and conquer Popstar.

Kung Fu Panda

• A Different Lesson: Heian Chao, the Ancient Evil Sorcerer and Kung-Fu Wizard who wishes to possess and control the chi of every person in the empire (and the empire itself), fulfills this role for the story. Xiu, eldest of the Wu Sisters, may be the character who gives the heroes the most personal trouble, but she is actually The Dragon. It is Chao who is behind all the schemes and plans the heroes must thwart, who personally hires the Sisters to kill Po and help corrupt Tai Lung back to The Dark Side, who possesses Vachir and Monkey in order to murder countless innocents and spread a Hate Plague over the Valley, and who directly taints the Pool of Sacred Tears so that he can control everyone in the Valley. He's also, of course, the Final Boss the heroes must face in the climactic ending battle.
• Shen vs. Kai: The true Big Bad is revealed to be the demon Hei Yinying, who is responsible for the creation of the Alternate Universe where Shen and Kai go to war against each-other all as part of Yinying's plan to usurp control of the Underworld for himself.

The Legend of Spyro

• The Legend of Spyro: A New Dawn: General Grendel turned out to be the Man Behind the Man to Tyrania and Kaze, having manipulated them to work with his plans for revenge on the Dragons and getting Pyrus out of the picture. To some extant, he's manipulating Deadlock, but it's mainly permitting her plan so she stays out of his way. He's now proceeded with his own plot for revenge against the Dragons. In the end, after Deadlock is defeated and makes a Heel–Face Turn, Grendel becomes the True Final Boss by performing a ritual giving him the power of the Naga Spirit Of War.

The Legend of Zelda

• The Legend of Zelda Ocarina of Time (DragonRand100): Ganondorf isn't content to just sit and wait while the hero defeats his minions and comes to challenge him. He actively tries to stop Link and his allies and he isn't beneath murder.
• The Legend of Zelda: The Sage of Darkness: Davik, the titular Sage of Darkness, manipulates Link into giving into hatred and anger in order to speed up Ganon's revival, intending to use him to end the Cycle of Eternity.
• Lost Isle: Morlach, a demon responsible for killing nearly every human in the titular isle who works to destroy the seal that keeps him imprisoned so he may begin his bid for global conquest.

Logical Journey of the Zoombinis

• Saetwo's Story has Romelau the leader of the Fleens, who also sent the Bloats to conquer Zoombini island.

The Loud House

• The Heroverse has a main villain in each of its stories.
  • Ace Savvy: A New Hope: Lord Tetherby, the man responsible for Ace Savvy's death, wishes to carry out his nefarious plans on Royal Woods.
  • Power Chord: High School Musical: The person behind the strange behavior of the students, filling them with negative emotions and causing them to reveal their deepest secrets. It’s later revealed it was Luan who was behind it as revenge for her mistreatment.
  • Nova: Homecoming: La Cobra, the leader of a vicious gang in Great Lakes City.
• It's a Kid's World: Each storyline has one, but the primary threat of the story as a whole seems to be the zombie army and its mysterious leader who turns out to be Boris Durvil AKA Lord Viribus.

Love Hina

• For His Own Sake: Naru Narusegawa, Keitaro's girlfriend, is here the ringleader of Keitaro's abusers, and sets out to make his life hell when he makes an effort to leave. It is slowly made clear that all his other abusers, even Motoko and Granny Hina, are being influenced by her. Later, Kagura Hajime and Chisato Ichimura, two girls from the pasts of Keitaro and Nagisa, show up and slowly hijack the plot, eventually forming a Big Bad Triumvirate with Naru for one last revenge plan involving kidnapping Keitaro.

Marvel Universe

• Breaking the Deal: Mephisto, who has used his deal with Peter Parker to gain more power and now plans on finding a way to conquer the entire multiverse. He also kidnaps Mary Jane in order to ensure that Spider-Man doesn't interfere with his plans.
• Civil War Hulk has Loki, with Baron Mordo as The Dragon. It turns out that they engineered the Scarlet Witch's breakdown, manipulated the Illuminati into exiling the Hulk, and played both sides of the superhero civil war in order to render the Earth defenseless towards their plans to Take Over the World.
• Polarity: Dormammu, the mastermind behind the zombie outbreak plaguing the Marvel Universe.

Mermaid Melody Pichi Pichi Pitch

• Mermaid Melody Pichi Pichi Duo: Dr. Hishki, a Mad Scientist who seeks to expose mermaids to the world and make himself famous.

Minecraft

• Minecraft Endventures: The Endermaster is the ruler of the End and the Enderman, and the one who started the Enderman invasion.

Miraculous Ladybug

• Nymph and the Corrupted Miraculous: Xue Ying, a former guardian who is corrupting the Miraculous jewels for their own goals.
• Miraculous: Uncertain Future: Hawk Moth, who in this fic is Lila Rossi, is the one who starts the conflict with her massive attack on Paris that kills most of the heroes.

My Hero Academia

• Apotheosis (MHA): Izuku Midorya/Apotheosis, who after having his dreams crushed by All Might, creates his own Infinity Gauntlet and intends on recreating Hero Society in his own image.
• Blues Drive Monsters: While Shigaraki and the League are the ones who set the plot in motion and Metalhead and her gang are the most prominent threat, it's Minister Osamu Nakayama and his Ministry of Individuality that appear to be the main threat. They authorized the Yard and Nakayama intends to exploit the current events to eliminate any autonomy of the Pro Heroes from the government.

My-HiME

• In Perfection Is Overrated, while the Obsidian Lord, the canon antagonist, is still active, The Usurper directs the SUEs in their efforts to defeat the Himes. He even possesses the Obsidian Lord, but is killed after his minions are defeated and the Obsidian Lord is forced from Reito's body. In the Chapter 17-19 arc, Ishigami, Nagi and the Bachiko and Meiko pair all put their own plans into motion.

My Little Pony

• Aurora (PonyholicsAnonymous) has Dawnbringer, though he's carrying out a plan devised by Discord, making the latter the Greater-Scope Villain.
• The Assassination of Twilight Sparkle: Prince Blueblood, who is responsible for the titular assassination. However, the sequel reveals his father, Amadeus Bluehood, was the Man Behind the Man who manipulated him into carrying out the assassination in a bid to get the Traditionalists and the Progressives to destroy each other, leaving the Blueblood family free to rule Equestria.
• The Captain Goodking Saga:
  • A series of unfortunate events that leads to another redeemed villain, yay!: Lord Sanies, being the one who engineered The Storm King's resurrection in the first place.
  • Captain Goodking and the Nightmare Knights: Sacanas, who lured the Nightmare Knights to the maze so they can play his little game.
  • The End of Time: Kronos, who wants the Seals of the Planets to himself.
• CRISIS: Equestria: Silvertongue, the ruler of New Pandemoneum whose ultimate goal is to reshape the multiverse into a world of absolute harmony...with him as its supreme ruler. Although he turns out to be The Dragon to Greater-Scope Villain Nihila. Until chapter 25, when he betrays her and steals her power, making him the definite Big Bad.
• The Dashverse:
  • Rainbooms And Royalty: Nightmare Moon, who just like in canon is attempting to usurp Celestia and bring about The Night That Never Ends.
  • May The Best Friends Win: Trixie. She's not really evil, but her attempts to drive a wedge between Rainbow Dash and her other friends drives the plot.
  • Hot Heads, Cold Hearts, and Nerves of Steel: King Sombra, who abducts all of Ponyville's foals so that he can drain their life forces to fully resurrect himself.
  • Wedding Bells Bug Hunt: Queen Chrysalis. As in canon, she's using Shining Armor and Cadence's wedding as a cover for her plans to invade and conquer Equestria.
• The Dear Sweetie Belle Continuity:
  • Feather Duster serves as this for the "Dear Cutie Mark Crusaders" arc; despite technically being a flashback-only character, he caused an immense amount of trouble which shaped the CMC's future lives to varying degrees. He also attacks them in the present in "Cutie Mark Crusaders Dream Warriors" before being Killed Off for Real.
  • In The Changelings Have a King, Chrysalis and Carapace (a.k.a. the transformed Prince Blueblood), the eponymous king, oversee the changeling hive's planned invasion of Equestria. That said, Carapace is much more The Heavy, taking the lead in both forming and carrying out the plan, while Chrysalis seems more concerned with her new brood (and it's hinted that Carapace is isolating and manipulating her).
• The Elements of Friendship:
  • Book 1: Harmony: NightMare, who the Mane 6 must defeat after she plunges Equestia into eternal night and banishes Queen Celestia to the moon.
  • Book IS [interlude one-point-five]: Bonds: Trixie, who uses the power of the Alicorn Amulet to kidnap the Queen of the Night.
  • Book II: Chaoskampf: Discord, who escapes from his stone prison and disposes of the Elements of Harmony, forcing Twilight Sparkle and her friends to go on another adventure.
• In The Elements of Harmony and the Savior of Worlds, after almost thirty chapters of buildup and foreshadowing, it turns out that Tirac is the one responsible for Luna's corruption into Nightmare Moon, and in the present is now plotting revenge against Megan.
• The Lemony Narrator of Equestria: A History Revealed seems to think that Celestia is the evil behind it all, and never lets the reader forget it. But this thinking is just due to her clear bias, a more fitting Big Bad would be the Nightmare Forces who were behind the Equestrian Civil War, birth of Nightmare Moon, and the Second Battle of Canterlot.
• Equestria Chronicles: Celestia, who has gradually become a paranoid, tyrannical dictator in her search for the Lunar rebels.
• A Future of Friendship, a History of Hate: Ruinate, the long imprisoned evil member of the Sentiox who, upon excape, intends on making Equestria into a Crapsack World before eventually destroying the rest of the universe.
• Getting Back on Your Hooves has Checker Monarch, Trixie's sinister sister, who spends the fic doing everything in her power to ruin Trixie and her quest to rebuild her life.
• How Trixie (Somehow) Saved Hearth's Warming has Leidr, who's buried the North Pole in snow and ice (it's a Homage to old school Christmas Specials) and is the one Vixen needs Trixie's help to stop. He's also a mutant, sapient Windigo.
• The Immortal Game has King Titan, Celestia and Luna's Archnemesis Dad and the creator/original ruler of Equestria. He also happens to be a Social Darwinist God of Evil bordering on being a full-blown Eldritch Abomination, which is why the princesses sealed him away in the first place.
• The Big Bad of Inner Glory is Thael the Metaspecter, except he is a Red Herring; the real villain is Seren, the alicorn of vengeance.
• The Legends of Equestria continuity introduces The Emperor, the lizard-like leader of an ultra-advanced race that controls a planet-wide empire, of which Equestria is "but a speck". When Celestia and Luna first overthrow Discord, he shows up to assert his control. Being unable to defeat them in single combat, he vows to return with his army should they ever lose control of the kingdom. That said, he is more of a looming Greater-Scope Villain for the two Acts which so far compose the story, with the ambitious technocrat Seraph directly taking this role instead for Act I, while in Act II the increasingly paranoid and controlling Celestia takes over.
• In the beginning of Loved and Lost, an extended retelling of "A Canterlot Wedding", Prince Jewelius steals Equestria's throne right after he has helped Twilight Sparkle in stopping the Changeling invasion by manipulating the public and Twilight herself to turn against the princesses, Shining Armor and Twilight's friends, banishing them all from Equestria as hated pariahs. They then spend the rest of the story trying to earn back everypony's (especially Twilight's) trust and expose an unbelievable truth they learn about "Holy King Jewelius I"; he himself told Queen Chrysalis about his cousin Cadance and Shining Armor's wedding and stroke a partnership to take control of Equestria with Chrysalis. He helped her sneak into Canterlot by telling her how to enter the caverns underneath the castle, and he lured Cadance into a trap, allowing Chrysalis to take her place. However, after making himself a Love-Interest Traitor for Twilight, he double-crossed the Changelings at the last minute. After the heroes defeat the army of Jewelius — who's been exposed as a monstrous fraud to everypony — and corner him in the final battle, he's killed by the Changelings for his betrayal. Queen Chrysalis then attempts to take the main antagonist role back, only for Cadance and Shining Armor to finally give the Changelings their canon defeat that has been delayed only because of the plot twists caused by Jewelius.
• Marionettes begins with Cover Story and Gear Shift as the main antagonists, pursuing and trying to capture Trixie. However, it's made clear early on that their organization is far larger and they answer to somepony higher up. The true Big Bad is Director Masquerade, the leader of the Stallions in Black, who takes over this role after the two are defeated.
• My Brave Pony: Starfleet Magic:
  • My Little Unicorn/My Brave Unicorn: Star Fleet Magic and My Brave Pony: The Movie: Titan, a sorcerer banished to another dimension 1000 years ago who's out to take over Unicornicopia.
  • My Brave Pony: Star Fleet Magic II: Queen Chrysalis, who attempts to throw United Equestria into chaos with her army of mimics.
  • My Brave Pony: Star Fleet Magic III: King Sombra, who's on the hunt for the pieces of the Crystal Heart to use for his own evil intentions.
  • My Brave Pony: Starfleet Humans: Sapphira, the leader of the Crystallites who intends to enslave the human world.
  • My Brave Pony: Star Fleet Magic IV: The Dark King, the future conqueror of United Equestria who travels back in time to ensure that his rule comes to pass.
  • My Brave Pony: Star Fleet Magic V: King Pinsar, the leader of the galaxy conquering Insecto Armada who has set his sites on United Equestria.
  • My Brave Pony: Star Fleet Magic VI: Windy Bag, who wants to bring back the old Equestria, by freeing the Equestrian ponies from their brainwashing and driving Starfleet out. Which is bad apparently.
  • My Brave Pony: Star Fleet Magic VII: Sienna, who leads her pirate gang in invading United Equestria for the Elements of Chaos.
• The Night the Magic Died: Gralo, an evil Krassau who desires to absorb all magic in Equestria
• Pages Of Harmony and its sequel, Empress Of Harmony, have Twilight Sparkle as a Well-Intentioned Extremist who does scientific procedures on her friends and kills them to preserve Harmony because Utopia Justifies the Means.
• The Pieces Lie Where They Fell: There is one, and it's the reason a new generation of Bearers are needed. It turns out to be the Power known as the Nightmare, which had once possessed Princess Luna and was now controlling the King of Equestria.
• The Pony POV Series is an interesting example: while Discord is only the direct Big Bad in certain Story Arcs, he's also the Greater-Scope Villain of the series as a whole, as even the arcs where he doesn't show up in person are still all the fallout from his actions in canon and the Back Story and there's also a subplot running through the series about his backup plan to escape his prison again. For the sake of precision, we'll break it down by arc:
  • Naturally, Discord himself in the original Discorded Ponies series, as it's set during his canon appearance. This also includes the alternate ending Epilogue (eventually expanded on in the Dark World arc), which shows what would have happened had he actually managed to win.
  • The Reharmonization arc has Loneliness — maybe not the arc as a whole, but the subplot about saving Trixie, which runs through a good chunk of it.
  • The Pearls arc has Princess Gaia/ Nightmare Whisper, Fluttershy's Superpowered Evil Side.
  • The "AJ's Dream" two-parter has Nightmare Mirror, Applejack's Alternate Universe Superpowered Evil Side.
  • Strife, Discord's sister, could arguably be said to be the Big Bad of the Generational Transition arc, as of all the Draconequi she was definitely The Heavy of the arc, and also served as the Final Boss for the last survivors of the Gen 3.5 universe. Though, she was just doing her job and was trying to give them a chance to prove their right to exist.
  • Discord takes center stage again in Origins, due to it being his Start of Darkness.
  • The Mind Games arc has Discord again as he manipulates Diamond Tiara into freeing him.
  • The Dark World arc returns to the Bad Future and thus Alternate!Discord is still the Big Bad. Considering we're seeing it from a Villain Protagonist perspective at first, Queen Cadence could also count as having been one in the past. Meanwhile, the Valeyard's Final Speech implies Discord isn't the only Big Bad... It now appears to be the Nameless Passenger, which is shaping up as The Corrupter (especially to Twilight) and a Knight Templar willing to sacrifice anything to defeat Discord. This entity ultimately ends up as the Final Boss and reveals itself to be Nightmare Eclipse/Paradox, an potential future incarnation of Dark World!Twilight who was consumed by her hatred of Discord, condemning him to a time loop that always ends in his death, followed by Twilight's transformation and the reseting of the loop, destroying each version of Dark World.
  • Shining Armor's arc has General-Admiral Makarov of the Hooviet Empire in actuality, an Equineoid Abomination called the Shadow of Chernobull. Though there's also the Wolf, an Animalistic Abomination that sees Shining as a threat to the timeline and wants to erase him.
    • Makarov ends up erased by the Wolf, which then takes over the role of primary threat, as it's still after Shining.
  • Queen Cocoon serves as this (in an Evil Versus Evil way) in Chrysalis' Origins Episode.
  • Chrysalis herself is the Big Bad of the Wedding Arc, as per canon.
  • Several stories in the Gaiden: 7 Dreams/Nightmares collection have antagonists:
    • Patch's story has several villains over the course of her quest for the Rainbow of Light fragments, but the most prominent are Film Critique, Basil, and Grogar, who serves as Final Boss.
    • Melody's story has Sharp Spear, whose Fantastic Racism towards Earth Ponies makes him a threat to Melody's family, especially once his son and her daughter become Star-Crossed Lovers. (Though he does eventually have a Heel–Face Turn.)
    • Bright Eyes' story has the Shadow of Existence of Discord's brother D___t, who briefly poses as her Enemy Within Cruel Eyes, and tries twice to absorb her soul and potential Concept in order to reconstitute himself. He also spends the entire Nightmares section stalking her as a presence she feels lurking over her whenever she feels emotionally vulnerable.
    • Clover's story, after a few wannabes, gets the closest thing to main antagonist in the shape of The Master — no, not that one, who also exists in this universe. This one, who turns out to be a Diamond Dog named Fluffy the Terrible posing as an old unicorn, uses an army of ponies he conditioned as orphaned foals to run a slave-powered mining operation that Clover's family eventually stumbles on. And he proves how dangerous he is by killing Scout. That said, her Final Boss ends up being a group of Eldritch Abominations so dangerous that Fauna Luster and Entropy worked together to seal them away, and who try to trick Clover into freeing them.
  • Discord, Umbra Breeze/Nyarlathotrot, and Nightmare Diamond Tiara are the Big Bad Duumvirate for the Finale Arc with their plan to rewrite the world into a grimdark Crapsack World. Nightmare Eclipse's surviving followers would also try to merge the Halflights back into their Twilight. And things circle back to Discord and Nightmare Nhilis, both trying to claim the title of Big Bad... not for power.. but so they can take all the BLAME. Then Havoc's insane avatar, Paxphobia, ends up being the True Final Boss as it breaks free of Discord's control as his change of heart weakens his grasp on it.
  • One could also argue that even when Discord is the Big Bad, the series still has a Greater-Scope Villain in his father Havoc — after all, he's the one who created Discord in the first place, and is also responsible for pretty much everything he's done in Equestria since he fed Discord his own brother (as well as Havoc's own avatar) in order to increase his power, before having him reborn in the mortal world. He was also the Disc-One Final Boss of Origins. Though it should be noted this is an insane Avatar of Havoc, as the true Havoc thought said Avatar was insane for doing it, the actual Havoc's actions, while a bit extreme from mortal standards (but grounded in his standards as the patriarch of Nature's Fury), were ultimately well-intentioned at worst and would never have condoned the things his avatar did when it went out of control. Under normal circumstanced, Havoc is ironically a Big Good for the setting.
• The Pony POV Series Chaos Verse (an official spinoff of the Pony POV Series) has Nightmare Phobia. Interestingly, in addition to being the main antagonist of the story, she's also stated to be behind many events of canon by manipulating ponies (including the Mane Six) through their fears.
• The Powers of Harmony: After a lot of buildup, the mysterious entity Cetus reveals herself as the main antagonist. She turns out to be Nightmare Moon's Echo, and is planning to take over Equestria and then to complete Nightmare Moon's goal. Subverted since the entire sequence of events is part of Harmony's scenario for strengthening the Element bearers and preparing them for Discord's return.
• Principal Celestia Hunts the Undead: The lead vampire, who turns out to be none other than Abacus Cinch.
• RainbowDoubleDash's Lunaverse's overall Big Bad is Corona, the struggle with whom forms the series' Myth Arc. However, as she's left severely weakened in Season 1 by her first confrontation with the Elements of Harmony, she ends up sharing the role with the cabal of corrupt Night Court nobles led by Duke Greengrass. But with their defeat in At The Grand Galloping Gala, Corona is free to take back sole Big Bad duties in Season 2 as she increasingly regains her powers.
• Re:Harmony has Chancellor Posey. Later on, the Empress Commander of the Pegasai and [[Chrysalis come in, making this this a Big Bad Ensemble.
• Shanghai'd! has General Verulius Constantine; the changeling Half-Blood Tyrant, with Queen Chrysalis and Leere as the Greater-Scope Villain.
• Through The Well Of Pirene has the King of Wands, Nessus, an absolute mountain of a centaur intent on fulfilling an ancient prophecy and 'shaping the world to come'. Rumors of his death via hydra-venom-soaked arrow in Greek mythology were greatly exaggerated.
• The Two Sides of Daring Do: Ahuizotl, who tries to steal the Princesses' power and use it to destroy all of Equestria.

Naruto

• The Element of Time: Madara and Obito are already around to cause trouble with the Jyuubi from the very beginning of the story, as per canon, and they still continue to cause trouble over the course of the new timeline. Raizen makes himself a brand new active threat for Naruto and Felix to worry about not too long after the timeline is reset. And he, Madara, and Obito are later joined in by the likes of Orochimaru, Akatsuki, Pain, and various other villains from both Naruto's home dimension and the Elder Dimension.
• Gouki Namikaze in A Growing Affection is the ultimate Big Bad; he is Pein and Konan's second teacher and they are working for Madara on his orders, both to reign in Madara and to enable Gouki to take control of Madara's plan if it works out. In book 2 Madara was the Big Bad, before Gouki comes out of the shadows.
• Hakumei: Danzo Shimura, who has long since taken over Konoha after killing the previous Hokage and turns it into an oppressive Police State; with Naruto and the others aiming to rise up against him.
• Son of the Sannin: The Fourth Ninja War has Akatsuki, led by Obito and the remaining members, and Orochimaru, who provides the Edo Tensei zombies for the army, as the main threats for the Shinobi Allied Forces.
• War of the Biju: Tobimaru "Tobi" Uchiha, a descendant of the branch family of the Uchiha Clan and the disciple of Madara Uchiha woh seeks to revive the Ten-Tails so he can become its jinchuriki and rule over the earth.

Neon Genesis Evangelion

• Advice and Trust: Seele is a secret organization that intends to kill literally everyone and merge their souls to create a single being. They are literally the origin of all troubles in the story and the cause of all hardships that the main characters have faced and the pain they have endured.
• The Child of Love: Gendo. He was behind Asuka’s overwhelming arousal which drove her to sleeping with Shinji, and he schemed to turn her daughter—his own granddaughter!—into a biological super-weapon.
• A Crown of Stars: Jinnai, a bloody dictator that is using overwhelming military power to take over the ravaged, wrecked post-apocalyptic world. In "A Throne Of Bayonets" -the story that preceeds this one- he plotted overthrowing his superior Winthrop, and achieved his goal thanks to the the reluctant aid of the heroes Shinji and Asuka. However he is arrogant, paranoid, short-tempered and prone to lose control, so he is less effective than his predecessor.
• Evangelion 303: Seele, which is plotting to launch a nuclear strike against USA and other countries.
• HERZ: The secret organization SEELE. In 2015 they tried to culminate their plan to merge all human souls into a single being. They failed and spent the next twelve years trying to build more Evangelions to carry out their goals, funding black projects and terrorist organizations.
• In Neon Genesis Evangelion: Genocide, Gendo keeps plotting the end of the world to reunite with his wife again, even though the war is over. His new schemes involving the Emerald Tablet, a strange and unpredictable computer program for which he has great plans, hurt his son and the other pilots again, forcing Misato to take drastic measures to protect her family. In the end, Gendo is supplanted by the Emerald Tablet, who has mutated into a mad A.I., hell-bent on its own version of Instrumentally.

Omen IV: The Awakening

• Always Visible: Doctor Baselard, who kills Delia, is mentioned in this way throughout the third act of the work.

OFF

• Bx: Execute has Death as the one manipulating the Harbringers, the tyrannical successors to the Guardians, and disguising himself as the friendly professor who guides you at the beginning; however, the Final Boss is Boxedman, the father of the Batters who Death extorts into fighting Ghost Batter.
• Continue/Stop/Rise has E, aka Epsilon, one of The Batter's former Add-Ons, now the ruler of Heaven who wants to fuse it with Earth and strip away everyone's free will in order to create a utopia.
• HOME (2013): The Batter reprises his role as this. Given that he's purified the world in a previous timeline, he intends to do it again, and it is up to The Judge to stop him.
• RENEW has Emmanuel, a Purifier and Suspiciously Similar Substitute of The Batter who takes it upon himself to destroy the world.
• RISE (Game) has Tate, the party's informant, who takes over Zone 4 and uses the Elsens there as his test subjects, bringing with him the specter invasion.
• UNKNOWN has Seneca, a tiny fox descendant of the Secretaries who intends to take over the remains of the world.

One Piece

• Mellorine! Mellorine!: Admiral Mardus and his Merchant Pirates, who are aware of what causes the gender-flipping and have been taking advantage of it.

Persona

• Persona: The Sougawa Files: The main villain is Nobuyuki Itou, the leader of the biggest crime syndicate in the city. He seeks to take over with the power of Shadows and rule over it with an iron fist, leading the city towards a "new age".

Pokémon

• The (Edit) War for Ash’s Freedom to not be Betrayed: Darkern Edgier is a mysterious masked man who tries to use the Book of Fate to reshape the anime-verse the way he wants, transforming Ash into a hyper-masculine, super-skilled trainer by having him undergo torment to harden him.
• Hypno's Lullaby: Hypno, who has been kidnapping children and forcing them to hurt and kill others.
• The Kaskade Region: Tom Bezzle, CEO of Amaze-All. He is dedicated to giving people what they want, whether they know it or not, and growing his MegaCorp to control all aspects of business and everyday life in the Kaskade region by any means necessary, whether it means dealing with unsavory criminal types, buying out newspapers that criticize him, controlling one of the four seasonal Legendaries, or even… making his own.
• Latias' Journey: Deoxys, the embodiment of evil who wishes to destroy all of reality and kill The Mother. The sequel has Oblivion's Shadow/Mewtwo, who wishes to release the Ruler of Evil trapped beneath the mysterious door under Treasure Town [[spoiler:so he can kill him once and for all.
• Nuzlocke Comics:
  • Season 1: Maxie. Closely following his role in the original game, he wishes to awaken Groudon to expand the continents, but loses control of the creature and nearly causes the destruction of Hoenn.
  • Season 2: Mewtwo. He lures Ruby to Kanto to trick him into breaking his seal, allowing him to leave Cerulean Cave and go on a killing spree.
• Pokémon Dark Rising: Darugis, the ancient entity Arceus sealed away eons ago who is now corrupting the world.
• Pokémon FireRed: Rocket Edition: Prof. Oak, who spends the game trying to use Red to get revenge against Lance and take control of the Kanto region.
• Pokemon Girls Hunter: Rylia, the current leader of Team Rocket, who’s out to enslave every girl in Puela she can for the sake of profit.
• In Pokémon Mystery Dungeon: Defenders of Warmth, Kuyurem, who not only is trying to eat the spirits of all who exist and is responsible for the deaths of all the humans-turned pokémon but also continues to threaten the land after being defeated.
• Pokémon Mystery Dungeon: Guiding Light: Zero, who spends the fic gathering the Time Gears so she can reset the timeline and prevent the gods from ever existing. It eventually becomes a Big Bad Ensemble between Zero and her former dragon Necrozma, with the latter aiming to straight-up destroy the universe in its entirety.
• Pokémon Mystery Dungeon: Lost Tracks of Time: Team Wish is responsible for the Distorted Floors taking over the mystery dungeons, the attacks on the Lake Trio, and brainwashing the Nobles. Their motivation is to resurrect their late trainer, Volo.
• Pokemon Mystery Dungeon Power Trip has Victini, who is A human who believes that the Alpha Preserve must be opened to humans.
• Pokémon Mystery Dungeon: Reflecting Balance: Erebos, a dark spirit possessing a Sigilyph who stole the Axis Tower crystals and hid them in different parts of the continent, disrupting the world's balance.
• Pokemon Opal And Garnet: Team Folklore, the villainous team of the Feluv region. As is explained in the "Bells of Notre Dame" Filk Song of their debut chapter, they want to capture the Legendary Pokemon of Feluv and use them to bring the entire region into peril.
• Pokémon: The Lost Child: For the majority of the story, Darkrai plays this role as the leader of The Brotherhood, which is responsible for much of the conflict. That is until he gets disposed of by his "father" and killed along with the rest of The Brotherhood.
• Pokémon Unbound: Zeph, the leader of the Shadows, seeks out Hoopa's power, and has the Shadows hunt down the Legendary Birds of Kanto for his schemes. In truth, he just wants Hoopa's power to try and bring back his deceased son, and his actions are out of desperation. Once Hoopa's power is unbound however, the real villain takes center stage: Aklove, who wishes to use Hoopa's power to activate the Ultimate Weapon and rain destruction on Borrius.
• Mr. X the Mewtwo in Pokéumans. Upon going mad (or perhaps not), he declared the transforming Pokeumans an impure species and sought to remove them from the world, with a sidelight to global conquest while he was at it.
• Ho-oh in Poké Wars, who is later forcibly replaced by his Evil Genius, Uxie who is a billion times worse.
• The Stardom Series: : Ardos is the leader of Reverse-Cipher, and intends to Take Over the World by spread his new XDrus and turning the world's Pokémon into Shadow Pokémon which he will control.
• The Sun Soul: Mewtwo, who uses the power of the Sun Soul to declare war on humanity in an attempt to eradicate it.

Pretty Cure

• Joyful Pretty Cure: Pinocchio, who stole the Kingdom of Toys' Reality; with plans to do the same to Earth's and permanently sever the bond between humans and toys.
• Olympus Pretty Cure: Nemesis, a spirit of revenge who's out to get the remaining Horoscorbs that prevent Olympia from falling apart.
• Pretty Cure Bukatsudo Energetic: Nocturna, the leader of Mora who wants the Dream Charm so she can steal the dreams of everyone in the universe.
• Roaring Hearts Pretty Cure: Sardonyx, the leader of the Void Clan who transforms Illuster's population into monsters and aims to create a world without will, dreams, or emotion.

Project Arrhythmia

• Black Heart: Jestar Heart is responsible for all opponents the player faces. All of the bosses in the first chapter are assassins sent by him to steal one of your three souls - which he intends to use the power of to take over the world.

Puella Magi Madoka Magica

• Fargo: Homura and the Incubators as a Big Bad Duumvirate. They operate and perpetuate the Magical Girl system, and as a result are the ultimate villains behind all or at least most of the story's happenings. They also hate each other with a passion, and much of the plot of Arc 2 serves as the arguable backdrop for their Cosmic Chess Game over who will remain in control over the magical girl system.
• A History of Magic: The Incubators, specifically the Incubator Directors, are the antagonists trying to turn girls throughout history into Puella Magi and Witches as usual, but on the other end is Pandora, a Puella Magi who became the first Angel, engineered all the despair in the world out of boredom, and wants to control/destroy humanity.
• Resonance Days: Reibey the Incubator is the true leader of the Void Walkers who uses Oblivion as his Puppet Queen and intends to capture Kyoko for his malicious plan to bring about Cessation of Existence for everyone in the afterlife.

Rango

• Old West: The plot is driven by Dufayel, a wealthy French-speaking fox who invested the Evil Plan of the movie's late Big Bad. He hires other villains to claim the heroes' properties — first legally, then more forcefully — because there's a great underground gold deposit which he was promised by his late business partner. Dufayel is desperate to claim it, especially because he's threatened by bankruptcy, a result of him investing nearly everything he had on Tortoise John's plan.

Ranma ½

• Hearts of Ice: Cologne. Spurred by her village's ultimatum, she will do anything to ensure that Ranma ends up married to Shampoo and dragged to Joketsuzoku. Her using blood magic to exile Akane to another dimension is only the beginning.

Resident Evil

• Wesker Lives: Albert Wesker, who survives his canon death and continues his plans of global conquest, but not before getting revenge on Chris Redfield and Jill Valentine.

RWBY

• RWBY: Destiny of Remnant: Just like in canon, Salem is the primary antagonist, serving as the Mistress of Grimm and being the root cause of the evil plaguing Remnant.

The Slender Man Mythos

• By the Fire's Light has the The Slender Man, who spreads chaos throughout the story and uses the people's belief in him to get stronger until he can cause the apocalypse.

A Song of Ice and Fire

• Of Gold and Iron: Petyr Baelish, the Night King, and the Faceless Men all share the title of Big Bad. Baelish is the mastermind behind Ned Stark's death, but he is the Disc-One Final Boss before he's disposed of by the Faceless Men. The Night King is the one who created the Long Night drug and unleashed it upon the whole of Westeros on the Faceless Men's orders, but he has his own agenda in mind.

Sonic the Hedgehog

• Memories of Infinite's Past: Clyde, Stryker's Rival Turned Evil and The Don of an organized crime group, who wants to kill Stryker and the whole squad.
• Nazo Unleashed: Nazo, a being made created by the negative energy of the Chaos Emeralds hunting down said Emeralds in order to gain further power and destroy everything he sees.
• Sonic.exe: X, the demon taking the form of Sonic that, in-game, kills Sonic and his friends, and outside the game kills people in the real world.

Soul Eater

• Soul Eater: Troubled Souls: Cancer Lucrenian, the head of Novus Partus who desires to complete Project Omega so that it can destroy the world and create a new one without hope. Furthermore, she is behind the creation of the Anria, a by-product of her long and extensive research.

SpongeBob SquarePants

• The Bikini Bottom Horror: The Tortured One, a Patrick Star clone who takes advantage of his regeneration abilities to kill everyone in Bikini Bottom. Until the epilogue, which reveals SpongeBob set everything up to eliminate Mr. Krabs and Plankton and be revered as a hero to effectively take over Bikini Bottom.

Star Wars

• I, Warrior has the enigmatic Sith known as The Master, who turns out to be a clone of Anakin Solo.

Storm Hawks

• A Raven Under the Starlight: Captain Dekutizonke of the Kitanen Empire is the main antagonist, hunting Master Cyclonis and Phoenix the Orange for revenge. He causes them a lot of pain in the last act.

Subnautica

• Aurora Falls has Baat Torgal, acting CEO of the Torgaljin Corporation on 4546B.

Super Mario Bros.

• Abducted Toad: King Purplius CVII is the tyrannical leader of the Purplians that Toad and Cappy want to overthrow in order to stop his plan to destroy the Mushroom people.
• Bowser's Last Stand: Bowser himself, now the Villain Protagonist, aims to take back his stolen castles from the Mushroom Kingdom and defeat the Mario Bros. for good. However, the real villain is the unnamed leader of Death Cap, the organization that took over the Mushroom Kingdom and the Koopa Kingdom.
• In Clash of the Elements this trope is zig-zagged a few times. At first Cackletta looks to be the main villain, but then Joe Dark takes over after Alex defeats her. Then this looks to be switched AGAIN in a case of Hijacked by Ganon and Demonic Possession via the Dark King only for Joe Dark to regain control, but then it is revealed in the epilogue that Cackletta is not only alive, but is working with Dimentio and Smithy, setting up possibly a Big Bad Ensemble, but then as it is revealed in Part 2, Both of them were Cackletta's pawns, meaning that she is the true Big Bad of Parts 1 and 2 all along.
  • This is also subverted in Movie 1. Tabuu was NOT the Big Bad, not even in the slightest
• Fallen Kingdom: Emperor Bowser, having successfully killed Mario, now rules over the remains of the Mushroom Kingdom as the Koopa Empire, and Luigi is the head of the resistance out to overthrow him. Until Chapter 38 reveals that Antonio/Grand Star, head of the Seven Stars, planned out the course of Mario and Bowser's conflict, with ultimate plans to converge the Star Children and create a world of silence where nothing in the world has powers.
• In Mario Brothers, King Koopa is this with his army of troops. He personally kills Luigi and plans to kill the Princess and Mario.
• Mario's Mystery Meat: Meat and vineRizon are the main threats. The former is the giant, wormlike Eldritch Abomination that swallowed Sponge, sparking his quest to escape, while the latter is a giant blocky head that represents Vinny's struggles with Verizon internet connection and the kidnapper of Princess Bleach.
• Paper Mario: Black Pit: Dimentio, who created the titular Black Pit for his own twisted amusement.
• Psycho Waluigi: Psycho Iris is the one who sends and accompanies Waluigi on his conquering journey, and has tried to conquer Unconcia in the past. He also becomes the Final Boss when he decides to destroy the world instead, prompting Waluigi to turn on him.
• Regular Pasta: Princess Peach is the entity tearing reality apart in order to ascend to godhood.
• Super Mario 63: Bowser, as always, is trying to take over the Mushroom Kingdom, this time with the help of the Orb of Power. Until it turns out the Orb was possessing him all along, and intends to destroy the world with a meteor.
• Super Mario 64 Land: Bowser, as usual. This time, he has stolen the Grand Ztar to power his army and try to conquer the Mushroom Kingdom.
• Super Mario 64: Last Impact: Rashay the Moon Spirit, who's trying to crash the moon into the Mushroom Kingdom for his own entertainment.
• Super Mario and the Dismal Heart: Count Bleck returns and has taken over the Mushroom Kingdom, kidnapped the princess, and recruited the Koopalings to help him destroy and recreate the world, and Mario must stop him. However, it is revealed after beating him that the titular Dismal Heart corrupted him into turning evil again.
• Super Mario and the Pearls of Wisdom: Tatanga returns and leads the invasion of the Mushroom World, intending to acquire the titular six pearls and use them with the Amulet of Krad to conquer the universe.
• Super Mario and the Sacred Bells: Bowser, as usual, is the antagonist who is using dark magic to invade the Mushroom Kingdom and wants the legendary gem — until it turns out that Dimentio was manipulating him all along so he could acquire a powerful gem and destroy the Mushroom Kingdom for revenge on Mario.
• Super Mario Dolor: King Bowser has once again kidnapped Princess Peach, and sends his minions to stop Mario from saving her. But Mario also has to deal with the Shadow Mario/Luigi, a Humanoid Abomination warping the Mushroom Kingdom into a nightmarish hellscape and stalking Mario. It is revealed to be an embodiment of his depression from the death of his brother Luigi.
• Toad Strikes Back: Kamek Koopa, the Identical Grandson of the original Kamek, steals the 7 Starspheres in an attempt to resurrect the long-dead King Koopa.
  • Toadette Strikes: Kammy Koopa, the Identical Granddaughter of the original, is the one responsible for the sleeping curse and commands the Koopa Clan, sending them to abduct the sleeping Toads. However, it turns out that she is not the only threat- Reckloo, the pair of eyes found in the hub worlds, is the true culprit of the sleeping curse so that nobody can bother him.

Team Fortress 2

• Cult of Personality. The Medic who leads oWn. The series begins with him being fired from the BLU team and forging his own organization. He's personally leading a campaign to destroy RED and BLU.

Teen Titans (2003)

• The End of Ends: Count Logan, who intends to use the Dark Prognosticus to destroy the galaxy until Beljar betrays him and takes the Dark Prognosticus so he can remake the universe in his own image.

Turning Red

• Turning Red: Secrets of the Panda: Jason Vaugn, the leader of the PCA, is the one responsible for hunting down the women in Mei's family who can turn into giant red pandas.

Undertale

• Dusttale: Chara has taken control of the game and is killing all the monsters over and over again for their amusement, but Sans, in order to stop them, has resorted to killing all the monsters himself to get the power to defeat Chara once and for all.
• Glitchtale has Chara in Season 1 after Frisk's Heel–Face Turn in the first episode (although W.D. Gaster briefly serves as an Interim Villain) and Bête Noire in Season 2 after Jessica Grey is revealed to be a Big Bad Wannabe in the first episode. In both seasons, the supposed Big Bad becomes a Disc-One Final Boss and the role goes to HATE, the Greater-Scope Villain.

Victorious

• The Princess and the Knight: Noxymis is behind the plot to frame Rosym for the kidnapping of Jadelyn, in order to draw out Victoria so he can get a gem her sister has and take revenge on the king of Rosym.
• The Wolf in me:
  • In the original fic, Livia is the vampire leader behind the kidnappings in the first story and wants to wipe out all werewolves. She's also responsible for the massacre of the werewolf royal family. Even when she dies, she still has an influence on the plot of the villains going forward.
  • Mr. X, really Claudia, is the antagonist of the rest of the series, being behind the plot to replace Jade with a demon, running the slavery ring in Prague, and seeking revenge on Jade for the death of her mother Livia.
  • Double Trouble: The alternate Beck Oliver is the alternate Jade's abusive boyfriend and the biggest enemy of the main Jade and Tori.

Yu-Gi-Oh!

• Yu-Gi-Oh! The Thousand Year Door has the Shadow Queen, whom plots to defeat the heirs to the Three Heroes who defeated her so she can escape her palace, unable to leave it until she does so due to the curse the Three Heroes placed on her.
• YU-GI-OH GX: Sleeping Beauty: Yubel, who upon going mad when Prince Judai fell in love with Princess Alexandra, embarked upon a quest to kill Alexandra and force Judai to love her instead and pursue the two throughout their lives. In the modern day, when Judai and Alexandra are reincarnated as Jaden Moto and Alexis Kaiba, Yubel returns to the human world to continue her pursuit, still seeking Jaden for herself.
• YU-GI-OH GX: The Wrath of Viper: Thelonious Viper comes back to haunt Jaden and the others, driven by a relentless determination throughout the story to kill Jaden for having defeated him and Yubel for betraying him and leaving him for dead.

Unsorted

• Ace Combat: Equestria Chronicles:
  • The Equestrian War has Red Cyclone, a malicious griffon soldier who, alongside his comrade Black Star, overthrows the good ruler of the Griffin Kingdom and plunges Equestria into a time of war. His reason for doing it is to enslave or kill all ponies, as he believes they are weaklings that spoil his ideal vision of the world.
  • Wings of Unity has Aurora Starlight, who was exiled from Equestria long ago for trying to forcibly become an alicorn and is now leading her fellow Exiles in conquering Equestria as revenge.
• All Worlds Alliance:
  • Chikage Tachibana, the high-ranking member of Apostles of the New World, is the one who instigates most of the conflicts across the entire All Worlds Alliance series and is the Arch-Nemesis of Chizuru Tachibana. However, his position as one tends to go between two ways: Firstly, he's actually the Dragon-in-Chief (after the reveal that he's answering to his higher-ups) since he's only taking the spot because of his superiors who are physically absent, who are serving as the Greater-Scope Villain. Secondly, there's the main fact that Chikage tends to be a part of the story's Big Bad Ensemble in several Mission stories.
  • All Worlds Alliance Missions - Tales of the World: Damascus, a member of the Apostles of the New World, orchestrates a plan in the wake of Lazaris' demise after Radiant Mythology 3 to steal the World Tree's mana so he can get a promotion to the Apostles as a Knight-ranking member.
  • All Worlds Alliance Missions - Madoka Magica: Kyubey the Incubator, who is responsible for the existence of Witches thanks to the Incubator system by turning girls across history into Magical Girls, and is the root cause of the conflict of the story. But then it turns out that he is a part of the Big Bad Ensemble with Chikage Tachibana, who appears to menace the All Worlds Alliance and Chizuru.
• Power Girl fanfic A Force of Four has Mars, the Amazons' ancient enemy. He plots to destroy Earth and relocate all souls to a kind of Valhalla where they'll fight eternally, keeping him forever fed.
• Agents of S.H.I.E.L.D.
  • The Season 4 Fan fics: Brett Petrie makes it abundantly clear to everyone that he is the biggest threat when he viciously tortures and murders both Andrew and Lincoln. After that, it's flat-out proven that the labels of Dragon-in-Chief and/or Dragon Ascendant truly don't stick because he always was using Ward as window dressing. He was never anything to Petrie but a misdirect.
• Ambition has Nightmare Moon, who has split off from Luna to become a separate threat.
• Bad Things Will Happen: Gengar. He's plotting behind King Boo's back, plans to take over both the Mushroom Kingdom and the Pokemon world, and wants to exterminate all humans.
• The fanfic Because I'm Not Popular I'll Try To Out With A hero pretty much has a rotating villains gallery, but the most recurring, and the one who causes the most trouble is Norman Osborn.
• The Big Time Rush fanfic Big Time Obsession has Hyde, the serial rapist/killer who terrorizes BTR (mainly Logan) and their friends througout the story. Turns out he is really one of many multiple personalities of Detective Simmons. And even in that case, Hyde tries to manipulate the other voices to his will.
• Calvin at Camp: Bowser Koopa, who is bent on destroying the titular camp.
• Examples from The Calvinverse:
  • Calvin and Hobbes: The Movie and Calvin and Hobbes III: Double Trouble have Rupert, the alien king of the planet Zok out to destroy Calvin, with Earl as his Dragon-in-Chief.
  • Can You Imagine That? and Trouble Island has Retro, who kidnaps children and attempts to use their imagination to take over the world.
  • The Pez Dispenser and the Reign of Terror: The good duplicate of Calvin who's out to destroy Earth .
• The Child of Love: Gendo. He was behind Asuka’s overwhelming arousal which drove her to sleeping with Shinji, and he schemed to turn her daughter –his own granddaughter!- into a biological super-weapon.
• The Big Bad of the Mass Effect fic The Council Era is set up as the Krogan Overlord, Kurvok. In fact, Kurvok is swiftly usurped by his advisor, Halak Marr, and Kurvok is dead by the end of Part One, while Marr is present until the very end of the series.
• For Cynical Classicist's Doctor Who fanfics, the War-Feeder is the most prominent villain in the stories feauturing the Eleventh Doctor and Norine.
• Double the Trouble: KAOS, the new leader of the Kremlings, has invaded the Northern Kremisphere, and to ensure the Kongs cannot interfere with his plans, has kidnapped Donkey and Diddy and sent his reptilian soldiers after Dixie.
• The Doki Doki Literature Club!/Doki Doki Literature Girls fanfic Enemies Within has Evil Sayori who serves as Sayori's Enemy Without who was created when dead Sayoris from different worlds combined and evicted themselves from the real Sayori when Monika rebooted the game. Her goal is to destroy every reality that the visual novel takes place in as a means of spiting Monika for her actions in the canon game.
• Evangelion 303 has Seele, an ancient secret organization that has manipulated the world for centuries and plots launching a large-scale nuclear strike against several countries to end up with their global influence.
• Frigid Future: At first it seems like Android 9/Commander Red is this, but he eventually gets killed by Doctor Gero/Android 20. Then Gero meets Cell, and when Gero dies, Cell quickly takes over as the Big Bad and Final Boss.
• In the first arc of Supergirl story Hellsister Trilogy, Mordru puts an army of villains together to keep the Legion of Super-Heroes busy while he looks to increase his own power. In the second and third arcs, Darkseid goes ahead with his plans to enslave all sentient beings.
• In Shazam! fanfiction Here There Be Monsters, Doctor Sivana puts a New Monster Society of Evil together to destroy the Marvel Family and take over the world.
• Hope for the Heartless: Arawn, the Death Lord of Annuvin and the former master of the Horned King. He was imprisoned in the Black Cauldron centuries ago, and when his former apprentice suffered the same fate, Arawn tortured him. When the Horned King is released for a onetime Redemption Quest, Arawn does everything in his power to ensure that the Horned King fails and is resealed in the Cauldron for him to eternally torture.
• Horseshoes and Hand Grenades:
  • Horseshoes and Hand Grenades: Ophiuchus, who's out to revive King Ouroboros in order to destroy all of humanity.
  • Month of Sundays: Neon Ulsland, the head of Foundation X.
• Carly Shay in iFight Crime With Victorious from a Bad Future where most of her friends and family were killed and she became obsessed with hording powers.
• Itadaki No Hecate: As of the second season, Southvalley is Yuji and Hecate’s greatest foe, as he plans to break the Masquerade and draw the entire world into the Haze-Denizen Forever War in a desperate attempt to finally win.
  • Shakugan no Shana: Eternity, by the same author, has the canon antagonist, the Snake of the Festival, after some Arc Villains are dealt with. He aims to create a perfect world for Crimson Denizens, and wants to destroy the current one to do so. Notably, unlike canon, he actually loses in the end.
  • Shakugan no Shana: Eternal Alliance has the Mouth of Power, a mysterious Malevolent Masked Man who controls the forces of Outlaw, with the intention of wiping out the entire Crimson Denizen race. It is eventually revealed that the true identity of the man under the mask is not a single person, but an entire Omniscient Council of Vagueness. Among their ranks are a Johan-lookalike called The Immortal and a woman who is implied to be Mare, the antagonist of the Shana PS2/DS game and the first two episodes of the second season.
• Keepers of the Elements: Radcliffe, an evil immortal wizard who wants to get rid of the Keepers so he can take over all of existence.
• Mortal Kombat: Desperation has Dark Raiden, who instigates a war between Outworld and Earthrealm out of nothing but revenge, but it slowly twists into a desire to become the God-Emperor of all realms known and unknown in Mortal Kombat.
• In Total Drama fanfic series Monster Chronicles Cedric usurps this position from Alejandro, becoming the main antagonist of the second half of Total Drama World Tour and of the story as a whole.
• The Resurrection of Rose has Rose the Hat as in the canonical novel and film. The Overlook Hotel also becomes a major player.
• The Road Paved in Concepts has Drosselmeyer, whose plot is ambiguous but it has to do with taking over all fictional universes.
• Shining Pretty Cure: Shade Queen, who seeks to steal the Star Pieces in order to restore her kingdom; with her willing to destroy anyone who stands in her way.
• Skylight Pretty Cure: Rapina Hawke, the alpha female of the Predators who are hunting down Tsubasa for being a humans-sanctuarian hybrid.
• Soul Eater: Troubled Souls has Massacre Queen Cancer Lucrenian. Two years prior to the start of the fanfic, she committed genocide against the Vladingham Family, a "legacy family" with close ties to Death Weapon Meister Academy, earning her nickname and the contempt of Lord Death. Now, she is working on something called Project 00000Ω: Omega to create a new world, one without hope.
• Sparkle Precure: Garnet, the leader of the Loveless who seeks to erase love from the world using the power of the Dark Gems.
• The Tainted Grimoire: Illua, the leader of the criminal organization Khamja.
• Team LVDR: Blaze is the main antagonist of the first volume, Zoe and August appear to be this for the rest of the series.
• The Uzumaki Tales: Return Of The Whirlpool is very interesting in that regard, as thanks to a lack of a Sorting Algorithm of Evil, several antagonists battle for the title of the big bad. Although Obito Uchiha is the one that caused most of the mess in the first place, Itachi Uchiha and Orochimaru are also sources of much misery and pulling many strings. Time can only tell where this will lead to.
• The Vizard Trilogy had an interesting variant. Each of the four stories has its own Big Bad, all of whom are part of the main group of villains, but the most involved in the overarching plot is Asayama Shiba. By contrast, her leader, Takeshi Katano, is a Non-Action Big Bad; he's the most powerful member of the villainous group and the leader of the Visoreds, but he barely does anything present-time, apart from sending an underling to save Ami and Rukia after a fight. However, the reason Asayama got so far was because Katano let her continue her machinations.
• Argath Iruvedla in Warriors of the World: Soldiers of Fortune, an undead soul-consuming anti-Norman megalomaniac Magic Knight. Believes that wiping out the humans would ensure a better future for the world itself, because he feels that he and the side he stands for is superior to humans.
• We Are What We Are has Starshot, a time-traveling Unicorn from Equestria seeking revenge.
• Weiss Reacts has Weiss' grandfather as the closest equivalent. He is the cause of the strife between Faunus and humans in-universe and is the reason why Weiss has a Dark and Troubled Past.
• In With Strings Attached, there are two: Jeft, who was responsible for all the crap in the Second and Third Movements, and Brox, whose machinations are responsible for the Fourth Movement.
• The Medaka Box fanfic World as Myth has a different Big Bad for each story arc:
  • In the first arc, we have Hanhaba Shiranui, acting as The Man Behind the Man for Koi Munakata.
  • For the second arc, it seems to be either Hanten Shiranui or Maguro Kurokami.
• The World of the Creatures has the Conceptivore - a creature made up of thoughts that can turn the world inside a person's mind into an actual physical universe. It does this so it can eat the new physical version of the person's mind.
• In YuYuGiDigiMoon, there are a number of main villains throughout the stories:
  • Season 1 (Wrath of Pharaohmon/Redux) has Pharaohmon. He possesses Lance Canebrook in ordering his minions to find ways in restoring his body to life. Upon his revival, he hosts a competition called The Shadow Tournament to tests his strength and remain on top to conquer both worlds.
  • Season 2 (Invasion of the Rajita) has Kaiser Ghidorah, a warlord of the reptilian Rajita race. He kickstarts an alien invasion on Earth in order to find both the Silver Crystal (which he killed Sailor Moon for) and the Moon Heart Crystal. His ultimate goal is to find the Romulus Source which will give him unlimited power and control of the universe.
  • Season 3 (Dawn of Chaos) has a shuffle of Big Bads. The Digidestined are facing Madoudramon and Valmarmon once he's revived. The Sailor Senshi faces Gamera. The Spirit Detectives faces Long and Arago once he's revived. The Duelists faces Professor Frank. Ultimately, the main villains are the Paradais duo: Sailor Charon and The Prophet/Millenniummon, who want to spread chaos throughout the multiverse.
• Zero 2: A Revision: UmbraDevimon and Demon both have their own plans to conquer both worlds; the Gravemon (an Expy of the Flood) want to absorb everything in both worlds; Piedmon briefly goes off on his own; Darkheart — Davis's Superpowered Evil Side — is created to serve as an agent of UmbraDevimon but eventually splits (more successfully than Piedmon) and starts tormenting the Digidestined for shits and giggles; Dragomon waits in the wings; and Myotismon is pulling strings from the shadows.

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