Big Bad Ensemble / Fan Works

• The author of the Homestuck fanfic series Academystuck stated that Caliborn, Jack Noir and The Empress (this story's version of Her Imperious Condescension) will be this somewhere along the lines, even mentioning this trope by name.
• All Worlds Alliance, especially the Mission stories, tend to have a villain ensemble in most of its stories including:
  • All Worlds Alliance Missions - Negima! has Chigusa Amagasaki, Tsukuyomi, Flirtare and Ikaruga. Chigusa is the primary villain of the first nine chapters but is relegated to Disc-One Final Boss and Big Bad Wannabe status when her threats pale in comparison to the latter three. Tsukuyomi and Ikaruga serve as the personal villains to Chizuru and Deku, as well as Erza and Setsuna, respectively. Flirtare, on the other hand, is the one actively aiding his Apostle cohorts in invading the world of Negima.
  • All Worlds Alliance Missions - Madoka Magica has Kyubey and Chikage Tachibana. While Kyubey instigates most of the conflict, Chikage invades the world of Madoka Magica, with the sole purpose of targetting his nemesis Chizuru. But both of them are in an Evil Versus Evil situation where where Kyubey was killed by him at the end of the story.
  • All Worlds Alliance Missions - Rainbow Rocks has Chikage again and the Dazzlings. While Chikage is there again to menace Chizuru, he's also in an Enemy Mine situation with the Dazzlings, whom he gives them an offer to fight the All Worlds Alliance heroes stationed in there, as well as with the Mane Seven. It is immediately clear that he and the Dazzlings have a different agenda, since Chikage affirms that he's not wanting the Dazzlings to join the Apostles at all.
  • All Worlds Alliance Missions - Monster High has Matthew Patel, Bartleby Farnum and Alligator McAlligator. Matthew instigates the invasion with his Apostles in the first half, while Farnum is after Frankie Stein to use her to awaken the Skull Shores' beast in the second half and Alligator serves as a personal antagonist to Chizuru.
  • All Worlds Alliance Missions - Friendship Games has Principal Abacus Cinch, Chikage and Midnight Sparkle Cinch is the one who instigates most of the conflict in her quest to start Midnight Sparkle's awakening, while Chikage disguises as Chandler Cheesecake to awaken Discord inside Funabori. However, Cinch serves as the threat to the AWA of the second half, while Midnight Sparkle is the Final Boss.
  • All Worlds Alliance Missions - CROSSOVERDOSE where on one end the Apostles are the Big Bad of the story, who are taking advantage of the chaos in the wake of the mass-disappearances across the multiverse so they can start their opportunistic invasion. On the other hand we have the mysterious man, who is the story's Greater-Scope Villain, being responsible for putting the entire multiverse in chaos due to him being the one behind the mass-disappearances, as well as the current cause of the All Worlds Alliance's problems in the present. Third is Silas Moron, who not only turns out to be alive, but he's the one responsible for mass-murdering the crew members of an unnamed ship, so he can resume his operations again by capturing living beings to be used as energy sources for his ship.
• Around the Clock at Bikini Bottom has the Overlord and Doodle Patrick, with the Overlord invading and taking over Bikini Bottom while Doodle Patrick is planning his own invasion.
• Avengers: Infinite Wars: Whooo boy. Does this big bad ensemble have a lot of heads.
  • First are the Separatists. The nominal enemy the Avengers have to help fight, but whose leadership is many headed and often working at cross purposes with them.
  • Second are the Sith, the true masters behind the Clone Wars. Their numbers are smaller, but work dangerously alongside the Separatists nominally.
  • Third is Ultron. A threat so huge that he forced and Enemy Mine for the entire galaxy when he announced his intent to kill them all.
  • Fourth are the ancient Force users. Another shadow organization, headed by old enemies of the Force like Getzarion the Nightsister and The Son of Mortis.
  • Fifth is Deathwatch. Though more of a Big Bad Wannabe, their presence drives most Manadalore-related stories.
  • Sixth are the Nightsisters themselves. While mostly neutral, the prompting of Wanda and Asajj leads them to start putting secret plans into motion to work against the galaxy as well.
  • And finally, while most Earth villains are Arc Villain foes for a few chapters, Baron Zemo is secretly forming The Masters of Evil in the background to challenge the Earthbound heroes in the absence of many of the Avengers.
• The Boys: Real Justice: There are a lot of villains in this fic, most only appearing in one or two chapters. However, there appear to be several overarching villains.
  • The Seven, with Homelander in the lead, take the primary role, seeking to retain their image in contrast to the Justice League. Homelander also has his own personal rivalry with the Boys and seeks to maintain control of his son Ryan.
    • Stormfront recently broke away from them after her Nazi beliefs were exposed, and gained the powers of Shazam.
  • The Joker is running around causing chaos and trying to spur them on. He was recently apprehended by Batman.
  • Circe slowly undermines Maeve's sanity and brainwashes her into going on a killing spree to spite Wonder Woman.
  • And behind the scenes, Lex Luthor, the Secret Society, and Stan Edgar of Vought Industries are working together to undermine all superheroes from both Earth-1 and Earth-7.
• Frozen Hearts (Red Witch): One one hand, you have Barton and the surviving humans whom are plotting to take over Ooo, on the other hand, you have the spirit of the crown that is trying to take over Simon's mind, and tries to return Ooo into a new Ice age, then you have Ash and the other wizards taking advantage of this commotion to rule over both humans and Ooo.
• In The Legend of Zelda series Bound Destinies Trilogy, Veress and the Interlopers are the more immediate threat, though Majora also influences the plot quite a bit.
• The Bridge (MLP) has two varieties of God of Evil who serve as Big Bads. Bagan, the Terran God of Extinction, and Grogar, the Equestrian God of Dark Magic.
• The Chaotic Masters:
  • On the one hand, there's the Chaotic Masters, who are trying to break free of their prisons and resume rampaging for fun. On the other, there's Tirek the Devourer, who engineers their escapes so that he can use the situation to further his own agenda of corrupting Raven into freeing their father.
  • And as a result of the crossover setting, there's numerous other villains running around outside the main plot — Wuya is accelerating her plans to regain her body out of fear of the Masters' return, Monkey Fist and Drakken team up to steal the Miraculous to buy their way into the Masters' service, and Daolon Wong is still carrying out his canonical plot to steal the powers of the Talismans.
• Cheshire (Miraculous Ladybug): Chloe and Hawkmoth - while Hawkmoth is the Greater-Scope Villain of the story, Chloe is the main villain on civilian side of Marinette's life.
• In Retro Chill: On one hand, we've got a Big Bad Duumvirate of Rupert and Retro trying to finally exact their revenge on Calvin, but Retro plans to betray Rupert, not seeing him as human. They replaced the original Calvin with an Evil Twin, but he is The Unfettered and quickly develops his own agenda, recruiting Jark and the monsters under his bed to destroy the world. And then we've got the Entity, who is manipulating all these parties for its own ends.
• Child of the Storm
  • Book 1 has first HYDRA, as led by Lucius Malfoy after he he kills former ally Baron Von Strucker, and their sort of ally Gravemoss, an immortal elven Ax-Crazy Necromancer and Omnicidal Maniac, who in practise does what HYDRA ask mostly to repay the debt owed for acquiring the Darkhold for him and/or For the Evulz. Meanwhile, Greater-Scope Villain Thanos lurks in the background and Chthon exerts more and more influence over Gravemoss via the Darkhold before eventually literally hijacking him during the Final Battle.
  • The sequel, Ghosts of the Past, takes this up a notch, courtesy of a more decentralized format, containing numerous Story Arcs with its own lineup of corresponding villains. While Voldemort (who got a body ahead of schedule during the first book) seems to be vying with Surtur to be the main villain of the story (Of Dungeons and Dragons features one of his minions), after his brief appearance in the second chapter he takes a backseat.
    • During the Forever Red arc, the main antagonists are the Red Room, led by General Lukin and Sinister, who want to use Harry to create a new generation of Super Soldiers and Harry himself as the Red Son, the Winter Soldier's Superior Successor... and face the Dark Phoenix, who wants revenge on them, at the low cost of everyone in his way (and probably planet Earth as collateral damage).
    • Then there's the Bloody Hell arc, which actually has two plots at the same time: in the Dresden storyline (which is this verse's version of Dead Beat), the Kemmlerites are still all competing with each other for control of the Darkhallow, but are also competing with the tenuous Villain Team-Up of Voldemort and Selene (the former promptly stabs the latter in the back as soon as he has what he wants). In the Harry storyline, the main threat is Dracula and his Grey Court, who want to kidnap Carol and drain her blood as a way to gain immunity to sunlight.
    • In the unnamed Smallville arc, the villain this time around is Dr. Robert Reynolds (true name Rudolph Jones) a.k.a. the Parasite a.k.a. the Void, who believes that people gifted with power (such as Clark) haven't "earned" it because they never had to work tooth and nail for their power, and never used it right or at all, and therefore, he feels entitled to take that power away from them because he "earned" the right.
• there’s several cases of this in the fanfic The dark never consumes all, for the light remains within its core, though thankfully they’re not all are on the same side. these include Lloyd Garmadon, Sons of Garmadon, Lila, Lord Garmadon, Hawkmoth, Pythor, his employer and the employer’s employer.
• Children of an Elder God: On one hand, there's Nylarathotep (representing the Outer Gods) who is manipulating the Children into being corrupted by the power they take from the Great Old Ones as part of the cycle he enforces on the universe. On the other, there's SEELE, who are seeking to use the Children to destroy the Great Old Ones as part of their plan to eliminate all of their master Cthulhu's rivals. And finally there's Gendo and Yui, plotting under SEELE's nose to use the Children's newfound power as a means of turning Yui into a god so that she can turn the world into a paradise.
• A Clash Of NEETS: The Children Of Destiny have more than a few Big Bads they need to contend with: the two biggest ones are the Lord Of Light Kefka Pallazo and his followers in the South, and the Great Other Arthas Menethil and his undead legions in the North; and that's not even counting all the usual suspects Westeros brings to bear: Stannis Baratheon, Littlefinger, Varys, the Ironborn, and any other petty schemer looking to seize power. Good thing they're not in it alone.
• Digimon Trinity features numerous antagonists. Takeru and Hypnos are out to protect the real world from rogue Digimon by any means necessary. The Nightmare Soldiers are carrying out numerous schemes to try and take over and/or destroy the real world. Lucemon shows up to try and steal the Hazard back from Guilmon, before going off to carry out his canonical plan (albeit entirely offscreen). And we haven't even gotten to Zhuqiaomon or the D-Reaper yet.
• Dragonball Z: Legacies features no less than five overarching villains, each acting independently with their own separate goals. First up is Varax, an alien warlord feared by just about everybody who wants Majin Buu's DNA so he can clone an army to conquer the universe and overthrow the Gods. Then there's Sentinel, a homicidal android Bulma accidentally created when she attempted to rebuild Android 16. After going rogue, he goes into hiding with plans to eliminate the Z-Fighters and Take Over the World. He ultimately succeeds at both in the Bad Future that Pan and Eva came from. You also have Kaiser Talos, an immortal supervillain who heads Capsule Corp's corporate rival and has long-term ambitions to make humanity into a Galactic Superpower. Meanwhile, there's the looming threat of Esdraelon, a primordial monster imprisoned by the Gods on an ice comet in ancient times and hellbent on killing everything in existence should it be freed. However, Orthros (real name Videl Satan a.k.a. Alter-Videl) overshadows them all. She's a nigh-omnipotent Dimensional Traveler who's been collecting thousands of Super Shenrons from different timelines as part of a plan to erase the entire multiverse and replace it with a singular, "perfect" reality built in her own image.
• Fairy May Cry: These combined worlds deal with the threat of the Demon Emperor Mundus who plans to liberate himself and conquer Earthland while seeking vengeance against the children of Sparda, the Black Wizard Zeref who has his own agenda and opposes Mundus, and the Black Dragon of the Apocalypse Acnologia who is revealed to have been the one to kill Sparda.
• Fallout: Equestria has four main villains: Red Eye, the Goddess, the Enclave, and the Steel Rangers, who all overlap each other and are all at odds. As the trope suggests they serve different purposes. Red Eye is an Evil Counterpart who forces Littlepip to confront what she really stands for. The Goddess is an Eldritch Abomination and Tragic Monster, exposing the evils the war created. The Enclave serves as an example of why no one tried to stop the war and why the wasteland is still a Crapsack World, being the ultimate example of Bystander Syndrome (the Delusional and Apathetic kind). The Steel Rangers force the main characters into questioning What Measure Is a Mook? (as one of their own is a Mook–Face Turn). In addition to this there is also the Arc Villain duo of Deadeyes and Mr. Topaz, who are unconnected with those four.
  • In the same vein Recursive Fanfiction Fallout: Equestria: Starlight has multiple Big Bads. In the order introduced they are Spark, Discord, Dusk Blue, Pride, and Nightmare Moon except it isn't really her, and the True Final Boss, Twilight Sparkle (who doubles as a Greater-Scope Villain).
• Power Girl story A Force of Four has three Superman's old enemies -Mala, Kizo and U-Ban- team up with old Wonder Woman's enemy Badra in order to destroy Earth and its heroes.
• Gargoyles and Turtles: Unsung Defenders: While David Xanatos and Demona are working together for now, Shredder and Ch’rell also have their own partnership where both alliances are working against each other as well as the Gargoyles and Turtles, even as the heroes have joined forces.
• In Golden Dawn: Lost Sunrise, the role of main villain is shared by Bonetail, a rogue who is building an army to destroy the Clans, and The Watcher, a mysterious villain from the prologue with mysterious intentions.
• Guardians, Wizards, and Kung-Fu Fighters has a truly impressive array of antagonists. As per W.I.T.C.H. canon, there's Phobos in full Evil Overlord mode, while Nerissa manipulates him and the rebels for her own ends. However, you also have Charles Ludmoore and his brothers also Playing Both Sides as well as manipulating events on Earth; Daolon Wong becomes The Starscream to Phobos; Bartholomew Chang and Harold Hale/King Arthur running the Dark Hand and advancing their own schemes on Earth; Tarakudo sitting on the sidelines building his power; and the master of the Cavalcade of Horrors using everyone as pawns to its own plans.
• Gundam Seed Destiny Altered: Durendal and Jibril are on opposite sides of the war, utterly hate each other, and both need to die in order for the story to end well. Which of the two is worse is arguable.
• Halloween Unspectacular uses singular Big Bads, or the occasional Big Bad Duumvirate, in the Story Arcs across its first seven editions. The eighth one, however, instead establishes a number of major antagonists. General Rausseman of PURITY, the Big Bad of the sixth and seventh editions, continues to act as the main antagonist, though until the climax he stays behind the scenes and leaves most of the legwork to his lackey President Fulton. Moreover, his actions have led to the rise of two separate forces determined to stop him at all costs — the Phoenix (willing to kill anyone even remotely connected to PURITY or Fulton's regime, even innocent voters) and Galactus (who is going to destroy Earth rather than let PURITY use its resources to conquer the universe). By the time of the climax, the heroes are left going up against all three of the above.
• The My Little Pony: Friendship Is Magic fanfic Harmony Theory has Nightmare Umbra, a boisterous War Godess, Social Darwinist, of unknown origin seeking to turn the world to ash and relies on brute force and intimidation to achieve her goals. In the other corner, we have Max Cash a wealthy and influential Chessmaster/ Magnificent Bastard, Bad Boss, and all around psychopath with a disturbingly upbeat Faux Affably Evil personality, seeking to obtain The Elements of Harmony to use for his own ends, and despite being a powerful magic user who can hold his own with half the heroes, relies mostly on manipulation and uses either his right hand mare and Dark Action Girl Charisma, or hired and often brainwashed goons to do the physical parts of his plans. About the only thing they have in common, is they're both very mysterious threats with as of yet unclear end goals.
• The Heart Trilogy has two main antagonists, Sauron and Fankil. While Sauron's pursuing his canon goals, he's also trying to coerce Smaug into becoming his beast of war. Fankil in turn pursues the dragon's love interest Kathryn to use her visions to locate the Door of Night and free his father Morgoth from the void. By the time of the trilogy's third part, the two evil entities exchange some information without technically working together.
• The entire concept of The Hellbound Hearts, a Disney fanfic where essentially all the former Big Bads come back for revenge, but they all have their own agendas, so it's hard to figure out which one of them will be the Biggest Bad.
• Hellsister Trilogy features two cosmic-level big menaces, Mordru who is determined to destroy the Legion and conquer the universe once for all, and Darkseid, who attempts to enslave the universe in the present, and when his scheme fails, lies in wait for one thousand years to and try to conquer the universe again by exploiting Mordru's own schemes.
• I Against I, Me Against You features the Director of Project Freelancer, the Meta, and Sunset Shimmer.
• Invader Zim: A Bad Thing Never Ends: Zim is still the Villain Protagonist out to conquer Earth, but then the second arc adds in several other rival threats — Tak wants to defeat Zim and conquer Earth for herself, Lex comes into conflict with Zim over possession of Minimoose, and Aldrich Coathanger is out to Take Over the City as a prelude to his main goal of harvesting enough Childergy to warp reality to wipe out all children.
• Jaune Arc, Lord of Hunger has Darth Nihilus and Cinder Fall. Darth Nihilus (or rather his Force ghost) is trying to corrupt Jaune to the Dark Side so he can take over his body. At the same time, Cinder is plotting to destroy Beacon Academy and steal the rest of the Fall Maiden's powers as per canon. Meanwhile, Salem is directing Cinder from the shadows as part of an overarching plan to divide humanity and destroy everything Ozpin has worked for.
• In the Jackie Chan Adventures and W.I.T.C.H. crossover Kage, Nerissa is following her canon plot, while also plotting to steal Jade's powers for herself. Meanwhile, the Queen is trying to corrupt Jade so that she can perform a Split-Personality Takeover, while Kur is plotting from the sidelines to manipulate Elyon into aiding his anti-shapeshifter plans. And then there's Yua and Ari, currently closer to Greater-Scope Villain status as they watch events unfold on Meridian, waiting for when they can step in and help Jade to fulfill the prophecy that she'll cause Kandrakar's downfall.
• In Darius Almighty's truely epic fanfic Kingdom Hearts III: Trials of the Keyblade, there're at least four factions of villains which Sora and his friends have to face through the story.
  • First is The Galactic Empire, led by Palpatine. Though for the most part, he lets his Co-Dragons, Darth Vader and General Darius, do the villainous dirty work for him while he himself rarely confronts the heroes.
  • Second is Maleficent leading another group of both Disney and non-Disney villains from her base of operation, Castle that Never Was, which she captured after Organization XIII's defeat.
  • Third is The Horned King leading the Tsviets while sharing a rivaly with Maleficent about who's going to harvest the powers of Kingdom Hearts first. Though after when Syndrome plays both sides, they both realizes the potential as an unstoppable force they can form if they join forces and soon forms a Big Bad Duumvirate together.
  • Fourth and last is the Chasers, Keyblade-wielding warriors who were Master Xehanort's followers during the ancient Keyblade War that caused almost the entire universe to fall to darkness. They're later on revealed to be led by a Not Quite Dead Xemnas.
• Kingdom Hearts New Epic has a triumvirate of big bads, though they're all opposed to one another just as much as they're opposed to the heroes, by and large. Alric Maynes has spent many years now trying to install his own corrupt dictatorship, on the basis of a political party, and has an Uday Hussein expy of a son. Then we have Wolfang Richler, the reality-crushing Physical God who is creating a Dark Alliance to topple the government of Alric Maynes above, so he can become "King of the Sky". And lastly, opposed to Richler by all appearances is the newly revealed Inverse Organization, white cloak wielding schemers who are...very vague, but definitely villainous, and are led by Minus Thirteen.
• The Legend of Spyro: A New Dawn has three Big Bads at the start, Deadlock seeking revenge on Spyro and Cynder for the death of her family (which wasn't their fault), Empress Tyrania seeking to conquer the Dragon Realms using Deadlock's plans to provide herself the opening to do so, and Boss Kaze who seeks to ransom Pyrus off for the highest amount of money he can. Kaze is only a direct Big Bad for Pyrus' storyline, however. In the end, it's revealed Deadlock's dragon General Grendel is actually The Man Behind the Man and was manipulating all the others for his own plan of resurrecting an ancient civilization destroying Eldritch Abomination to take revenge on the Dragons for banishing the Naga to the Unknown Realms.
• The Legendary Spider Man: There are many enemies around this universe. Kingpin is the foremost early Big Bad, someone always creating new villains and leading the criminal underworld of New York. However, there are others lurking around making moves. Hammerhead is acting on behalf of his injured boss, Silvermane. HYDRA is lurking in the background as an international villainous organization. Other international groups like The Inner Demons and The Hand have representatives working in New York. Otto Octavius continues to make moves in the background, which turn into grand plans. And then there's Norman Osborn, whose influence on the story extends to many villains' backstories, as well as lies in the middle of double dealing in both legitimate and illegitimate businesses.
• The Lion King Adventures:
  • Series One's main villains are Scar and Hago. Between the two of them, they're responsible for every life-or-death adventure Simba and Nala face in the season; they team up once mid-season, go their separate ways, then team back up for the last two stories on the season. At this point, Scar goes Ax-Crazy and proves to be Eviler than Thou... prompting Hago to kill him and become the true Big Bad.
  • In Series Four, Shocker is the most prominent villain, but it turns out that everything he wasn't involved in — and at least one situation he was — was orchestrated by the Vimela-possessed Mufasa and Sarabi. They prove so much worse that Shocker doesn't need too much prompting to team up against them.
• Season 1 of The Lunaverse, in addition to the overall series Myth Arc of the conflict with Corona, also focuses on a Story Arc of the Luna 6 dealing with the machinations of the corrupt Night Court (best represented by Duke Greengrass). However, this is dealt with in the season's last story, At The Grand Galloping Gala, allowing Corona to take over as sole Big Bad in Season 2.
• Appropriately, Mario & Sonic: Worlds Clash has Bowser and Dr. Eggman serving as Big Bad for their respective worlds.
• Aliens/Once Upon a Time fanfic Monsters: The Xenomorphs are led by the queen, which is the biggest psychical threat to the group, but Robin acts as the main human threat, trying to get the creatures back to Earth and being the cause you the current outbreak.
• Cortex, Uka Uka, Dr. Robotnik and Mario Head form one in Mashed Bandicoot. Unfortunately for them, they end up betraying each other until Cortex becomes the true big bad.
• In Nareto: The Scret of Shiobi, the role of Big Bad is shared between Danzo, Madara, Darkeye, and Apollo Justice. Wait, what?
• Neon Genesis Evangelion: Genocide: There is Gendo on one side, with SEELE opposing him. The latter eventually forms a Big Bad Duumvirate with the Emerald Tablet, though the Tablet eventually betrays them and pulls a Make Way for the New Villains on them.
• New Avengers has Sinthea Shmidt/Sin and Viper/Madame Hydra fighting for control over HYDRA.
• Paris Burning has several: Atlantis and his followers, the thing in Antarctica, and a large family of competing Eldritch Abominations.
• In Perfection Is Overrated, the Obsidian Lord, the canon Big Bad, and the Usurper serve as the main antagonists. In Chapter 17-19, a variant occurs with Ishigami, Nagi and the Bachiko and Meiko team being responsible for what happens. The Advisor/Avatar is revealed to be manipulating all of them, but is mainly in the background.
• Pokémon Reset Bloodlines: In the main story the candidates for Big Bad are Cyrus (for being the one who started the story's events), Giovanni (for being the most present), and the Bloodline King (who has been lingering around in the shadows but impacting the story heavily). Team Cipher is the main visible threat of the Expanded Universe oneshots and is hinted that they will join the main story ensemble later, while Team Galactic appears to be the overall Big Bad for the The Wild Boy of Sinnoh Spin-Off and, via Cyrus, a Greater-Scope Villain for Ash. And then there's Lusamine (from Pokémon Sun and Moon), who is manipulating events from the shadows (including keeping contact with Team Skull through Guzma) and is aware of Cipher's actions, not to mention hinted to play a large role in the Bad Future MissingNo showed to Ash.
• As of this writing, Pony Gear Solid features Macbeth, a pony revolutionary who wants to take over Equestria so he can restore its military. Alistair Cain, Commander of the Pegasus Wings PMC that's providing him with a Metal Gear. Trenton, a cyborg ninja who is working for the Patriots, who are conducting another iteration of the S3 experiment, this time using all of Equestria. And last but not least, an unknown dark force that appeared in Equestria roughly the same time as the humans known only as the Lord of the Flies.
• The Dark World arc of the Pony POV Series initially has only Discord as sole Big Bad, not counting an attempt by the Valeyard. However, the Valeyard's Final Speech and a few other things hint at the presence of a second force manipulating events in its favor. It eventually turns out to be the Nameless Passenger, the entity who's been manipulating Twilight and her friends from the start. She's revealed to be Nightmare Eclipse/Paradox, an alternate version of Dark World Twilight who was consumed by her hatred of Discord and trapped Dark World in a "Groundhog Day" Loop to punish Discord forever. This latter being ends up proving Eviler than Thou and acts as Final Boss following Discord's death.
  • Also the Shining Armor Arc. While Shining's Arch-Enemy is General-Admiral Makarov aka the Shadow of Chernobull, who wants Shining dead no matter what, the even greater threat (to them both) is the Blank Wolf, an Animalistic Abomination Clock Roach that sees Shining's presence as a threat to the timeline and wants to erase him. After the Wolf erases Makarov, it takes over as the primary threat.
• In the Jackie Chan Adventures fic Queen of All Oni, there's Jade, who is the main Big Bad of the story, and Tarakudo, who she intends to replace. Though he's more of a Greater-Scope Villain, due to still being sealed away at the moment. He gets loose during the Final Battle, leading to the two of them coming to blows.
• Remnant's Bizarre Adventure has both Cinder and Whitesnake (as of now). They're working together for now, but their goals are incompatible and irreconcilable.
• In Danny Phantom fanfic Resurrected Memories: Paulina and Vlad, Paulina is quick to get on Ember’s bad side and is the central antagonist of the prom storyline while Vlad has returned from space and is building an army in order to kill Danny and destroy Amity Park and with Spectra’s help uses Danny’s feeling’s for “Amberline” against him.
• SCP – Containment Breach: 174, 106, and 079 all want your head on a silver platter.
• In SlifofinaDragon's Sengoku Basara fanfics, starting from Let's Endless Party! to Finally Home, we have Toyotomi Hideyoshi, Mori Motonari, Oda Nobunaga (who had been briefly and unintentionally revived by his sister Oichi's magic), and Toyotomi's vengeful daughter Kagehime.
• Shadows Awakening is an interesting example, as it has two Big Bad Duumvirates (Daolon Wong and The Phantom, The Queen and Tarakudo) that just so happen to be opposed to each other.
• In the Jackie Chan Adventures and Teen Titans crossover fic A Shadow of the Titans the first arc sets up one of these between Brother Blood and Tarakudo, both of whom work to corrupt Jade, independently of each other, and for their own agendas. When they finally clash at the arc's climax, Tarakudo wins. And then there's the Greater-Scope Villain, the Cackler, who transformed Jade into a Shadowkhan and banished her to the TT universe in the first place, for reasons as of yet unknown.
• Spike's Gambit: On one end, there's the power hungry Impossibly Rich. On the other, there's Flim and Flam, the protagonists' sleazy and crooked bosses. That is until Impossibly took over the brothers' business and assets and becomes the main Big Bad overall.
• Soul Eater: Troubled Souls: Lord Death and his higher-ups have identified three primary threats: Massacre Queen Cancer Lucrenian, Arachne the leader of Arachnophobia, and Kishin Asura.
• Star Wars vs Warhammer 40K: The Invading Refugees from the Imperium of Man want to conquer the Star Wars galaxy in the name of their God-Emperor, convert all humans to the Imperial Cult, and exterminate all aliens and droids. The Sith led by Palpatine seek to destroy the Jedi and transform the Galactic Republic into The Empire. While the Imperium presents the larger and more immediate threat, the Sith are responsible for starting the war between the Republic and the Imperium in the first place. The second season's ending adds a third Big Bad candidate in the form of a rogue General Grievous, who has grown sick of being used as a pawn by the Sith and cuts off all ties with Dooku in order to form a CIS splinter faction.
  • The Imperium by itself could count as an example seeing as how it has numerous leaders and sub-factions who often act with their own agendas that put them at odds with each other. First there's Orion Phatris, the Space Marine Chapter Master officially commanding the invading Imperial forces, who plans to eventually conquer a section of the Star Wars galaxy so he can establish a bastion of Imperial culture there. Next up is Davik Thune, a rival Chapter Master who goes rogue at the start of the series and leads his own separate faction that wreaks havoc across the galaxy as they attack worlds belonging to the Republic and Separatists alike. Then there's the Inquisition, who blackmail Orion into leaving them alone and promptly go off to do their own thing, which involves infiltrating the Republic, hunting for Genestealers, and plotting Machiavellian schemes (sometimes against themselves). Last but not least is Tyranus Macharion II, an enigmatic Imperial Guard general who conspires to overthrow Orion and is responsible for orchestrating the Battle of Axum, which takes up the story's focus for the entirety of Seasons 2–3.
• The Stronger Evil, which starts off at the end of the Noble Animal arc of Jackie Chan Adventures, begins with the resurrection and subsequent reimprisonment of Shendu as well as his resurrector Daolon Wong's death by Shendu's hand. The Big Bad role is then taken over by Drago, the future son of Shendu and Valerie Payne who sets out on the Demon Chi arc until he accidentally releases Tarakudo who turns Jade back into her Queen of the Shadowkhan persona and sets out to regather his Shadowkhan armies as well as have his revenge on Shendu for imprisoning him, forcing Shendu and Drago to cooperate with the heroes. In addition to that, Hsi Wu plots to escape from the Netherworld and restore his corrupted connection with Jade, his Other. There's also a possible Greater-Scope Villain with creepy blue eyes that Shendu knows and fears, later revealed to be his mother, Tiamat.
• To Hell and Back (Arrowverse): As a result of having multiple leads who share equal focus, each have a corresponding Big Bad per arc/season(s), which all three cooperate to take down. For Arc I/II, Oliver's is Malcolm Merlyn, Barry's is False Harrison Wells / Eobard Thawne, and Kara's is her aunt, General Astra In-Ze. Of the three, only Eobard was aware of the other two's existences, due to being from the future.
• Total Shuffled Island Series
  • The first season features Alejandro, Scarlett, Jo, Amy, Sugar, and Scott, though only the former three have much lasting effect or make it to Action (though Amy comes in later), while Jo loses much of her antagonism in Action before being swapped out with Scott and Sugar for World Tour.
  • The fourth season features Courtney, Justin, and Noah with varying degrees of badness. Justin is self-centered, and uses his good looks and charms to sway the vote in his favor. Courtney, whose bossy and controlling attitude, plus her immense desire to win, antagonizes the other campers. Noah, who, while not outright a villain, is still ambitious enough to manipulate the others with mind tricks in order to keep himself in the game.
• The Upheaval Series has the following villains: Fenrir and the Wolven, Arugek and the Ursans, and Sesyth and the Ophidites make up the armies and races attacking Equestria, but then you also have Deceptive Disciple Black Rose and Greater-Scope Villain Oceanus. And let's not get started on all of the Dragons and Co-Dragons.... Knight Templar Gravitas also plays a major antagonistic role, but he's really more of an Arc Villain.
  • Recursive Fanfiction Legionnaires of Equestria introduces a new threat: the Arenea and their Queen.
• Vale's Underground features four different mob trades headed by Kenna Carter/"Cinder"^note "Cinder" is only an alias., Adam "the Bull" Taurus, Roman Torchwick, and the Branwen twins. All of them have a relatively equal part in the criminal underworld while gaining a monopoly on a specific trade, but each of them attempts to infringe on their markets. While they perform a temporary peace treaty to keep war off the street, they still compete for business. Cinder is the main Big Bad of the narrative, but that's only because Ruby Rose is focused on getting something on her since she is the only one who has obscured her real name.
• The Vampire of Steel has two big bads: M'Nagaleh and Kryptonian vampire Zol-Am, although their goals and plans don't overlap.
• Webwork starts off with a clear-cut Big Bad in the form of Tarakudo, as he manipulates Jade into being The Dragon and working to free him. However, as time goes on, she starts to realize that as Dragon-in-Chief, he needs her more than she needs him, and starts to slip more and more from his control. Meanwhile, Tarantula beings to act as The Starscream to Jade under the guidance of the Old Queen's spirit. And on top of that, recently we've seen several members of the Chan family Rogues Gallery unite under the leadership of an empowered Bartholomew Chang, following their own agenda.
• The Wolverine and the X-Men (2009) fanfic "Wolverine and the X-Men: Season 2" picks up where the original series left off, with Apocalypse as the upcoming and overriding threat and Mister Sinister as the Dragon-in-Chief and The Heavy since his master has not appeared yet. However, they're far from the only threat, since "Danger Ratings" adds The Human High Council, led by Cameron Hodge and General William Kincaid, who are acting in response to Magneto's actions at the end of the original series and will go on to oppose Sinister according to Word of God. The series also has Mojo as an Arc Villain for "Danger Ratings", with Omega Red out for revenge against Weapon X for some reason and Weapon X itself hanging around in the background.
• Almost every character and faction in Yognapped can be interpreted as the Big Bad, but Notch and Sben are the most prominent examples. The former is a Jerkass God who murdered his younger sister to keep his creations intact, then imprisoned his retaliating brother for centuries before killing him anyway, which destabilized Minecraftia and set the course for the Collapse, starting off the events of the series. The latter wants to properly destroy Minecraftia, and tries to accomplish this by flooding population centers with ruthless soldiers and unmatched firepower. It gets even worse once he's resurrected by Notch's aforementioned brother.
  • The Alpha Griefer also counts, though his tactics are much cleaner than Sben's and he has legitimate motivations for the destruction he causes. He points this out to Sben in a conversation, before one of his sleeper agents non-lethally shoots the latter in the back.
  • Towards the end of the series, even the heroic Lewis falls under this.
• Young Justice: Darkness Falls has this with The Light and Darkseid sharing duty. However, after Vandal Savage is Killed Off for Real, Darkseid takes over as the true big bad, though the light does get a few pot shots in as well, even if they're in the background for the rest of the fic.
• Young Justice Titans continues the trend with the Light sharing the stage with the Church of Blood. Whether they were partners at all in the past has yet to be revealed, though the Church of Blood is much more The Heavy at this point in the fic.
• In the Digimon story Zero 2: A Revision, after the Emperor arc is over, it dissolves into this: 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.

---