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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 BigBad is the one who turns out to be behind several other seemingly independent threats.
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* ''Fanfic/AceCombatEquestriaChronicles'' has [[spoiler: 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 [[spoiler: enslave or kill all ponies]], as he believes they are weaklings that spoil his ideal vision of the world.
* Gouki [[spoiler: Namikaze]] in ''FanFic/AGrowingAffection'' is the ultimate BigBad; 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 BigBad, before Gouki comes out of the shadows.
* ''{{FanFic/Alex}}'' has the titular antagonist herself from an ''WesternAnimation/AdventureTime'' fanfic. It turns out she's the BigBad of the animated series all along, commanding the likes of Ice King, Ash, and Door Lord to do her bidding.
* ''[[FanFic/AvatarTheLastAirbenderRevised ATLAR]]'' has Zotu and Azul's father, Aizo, set up as the BigBad 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 ''[[Fanfic/AzulaTrilogy the Azula Trilogy]]'', the overarching BigBad is [[spoiler: Zhan Zheng, the spirit of War]]. Each of the three fics also has its own BigBad:
** ''Heart of Fire'': [[WellIntentionedExtremist General Azun]]
** ''Path of Fire'': [[WoobieDestroyerOfWorlds Wei Ming]]
** ''Soul of Fire'': [[spoiler: Zhan Zheng]], possessing [[EvilOverlord Jian Chin]]
* In the ''FanFic/BattleFantasiaProject'', each 'arc' will have a big bad. As of July 2011, said Big Bads are...
** Arc One: The Nightmare Factory, headed by The Oneirovore.
** Arc Two: [[FateKaleidLinerPrismaIllya The Magical Alliance]], who want to discredit the infant Magical Girl Alliance, and 'disprove' magic as a 'silly supersticion' once more.
** Arc Three: [INFORMATION PENDING]
** Arc Four: The [[Anime/PuellaMagiMadokaMagica Incubators]], and whoever's in charge of them.
** Arc Five: [[Franchise/SailorMoon Jedite]] and a horde of Dark Kingdom survivors.
** Arc Six: [[Anime/MagicalGirlLyricalNanohaStrikers Jail Scaglietti.]]
** Arc Seven and Up: Little has been discussed beyond Arc Six. [[spoiler:That said, it seems to be the consensus of the board that [[SmugSnake Quattro]] from [=StrikerS=] will escape and come back as the Big Bad at a later time.]]
* The BigTimeRush fanfic ''[[http://www.fanfiction.net/s/7986375/1/Big-Time-Obsession Big Time Obsession]]'' has Hyde, the serial rapist/killer who terrorizes BTR (mainly Logan) and their friends througout the story. [[spoiler: 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.]]
* ''FanFic/BurningBlack'' at first seems to have Remy as it's central antagonist, but it eventually turns out that he's working with [[spoiler: the Pixies]], who seem to be using him as a means to fulfilling their own agenda.
* ''Fanfic/ByTheFiresLight'' has the [[TheSlenderManMythos The Slender Man]] serving as the head bad guy for the series.
* [[Franchise/SuperMarioBros Bowser Koopa]] often plays this role in ''FanFic/CalvinAtCamp.''
* Examples from Fanfic/{{the Calvinverse}}:
** Rupert and Earl serve this function in ''Fanfic/CalvinAndHobbesTheMovie'' and ''Fanfic/CalvinAndHobbesIIIDoubleTrouble''.
** Retro serves as this in ''Fanfic/CanYouImagineThat'' and ''Fanfic/TroubleIsland''.
** The good duplicate of Calvin serves as this in the RecursiveFanfiction ''Fanfic/ThePezDispenserAndTheReignOfTerror''.
* In ''FanFic/ClashOfTheElements'' this trope is ZigZagged a few times. At first [[{{MarioAndLuigiSuperstarSaga}} Cackletta]] looks to be the main villain, but then [[spoiler: Joe Dark]] takes over after Alex defeats her. Then this looks to be switched AGAIN in a case of [[spoiler: HijackedByGanon and DemonicPossession via the Dark King]] only for [[spoiler: Joe Dark to regain control]], but then it is revealed in the epilogue that [[spoiler: Cackletta is not only alive, but is working with [[{{SuperPaperMario}} Dimentio]] and [[{{SuperMarioRPG}} Smithy]], setting up possibly a BigBadEnsemble]], but then as it is revealed in Part 2, [[spoiler: Both of them were Cackletta's pawns, meaning that she is the true BigBad of Parts 1 and 2 all along.]]
** This is also subverted in Movie 1. [[spoiler: Tabuu was NOT the BigBad, [[{{WellIntentionedExtremist}} not even]] [[{{GoodAllAlong}} in the slightest]]]]
* Beyond Birthday becomes this in ''FanFic/ConstantTemptation'' after Light [[TheAtoner retires from villainy.]]
* The BigBad of the Franchise/MassEffect fic ''The Council Era'' is set up as the Krogan Overlord, Kurvok. In fact, [[spoiler:Kurvok [[TheStarscream 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.]]
* ''Fanfic/CrisisEquestria'': [[MagnificentBastard Silvertongue]] at first, though he turns out to be TheDragon to BiggerBad [[GodOfEvil Nihila]]. [[spoiler: Until chapter 25, when he [[TheStarscream betrays her]] and [[AGodAmI steals her power]], making him the definite BigBad.]]
* ''FanFic/CrownsOfTheKingdom'' has Maleficent, who controls the Dispirations. The final fight with her comes ''after'' the one with Chernabog.
* [[spoiler: [[DarkActionGirl V]]]] in ''FanFic/ACureForLove'' until her organization is [[HijackedByGanon Hijacked By]] [[HeelFaceRevolvingDoor Kira]].
* ''[[Fanfic/TheDarkLordsOfNerima The Dark Lords Ascendant]]'' has Tanizaki Kazuo, a CorruptCorporateExecutive who has big plans [[spoiler: to steal Sailor Moon's power]], and plays a game of XanatosSpeedChess to pit Ranma and the Nerima Wrecking Crew against the Senshi while he carries them out.
* Unsurprisingly, [[Series/BarneyAndFriends Barney]] serves as the main villain in the ''Fanfic/DayOfTheBarneyTrilogy''.
* ''Fanfic/DeathNoteEquestria'': As VillainProtagonist, the role falls to [[FallenHero Twilight]] by default. Though one could argue that [[{{Shinigami}} Mer]] takes on the role of TheHeavy (if not outright BigBad) during Twilight's MemoryGambit, even though everything is [[ExactlyAsPlanned going according to Twilight's plan]].
* Baal in [[http://www.fanfiction.net/s/6984913/1/Disgaea_Jewel_of_the_gods Disgaea: Jewel of the gods]]
** Currently, it seems to now be a BigBadEnsemble with [[MakaiKingdom Seedle.]]
* [[Anime/SailorMoon Mercury]], from Fanfic/DungeonKeeperAmi. [[BlatantLies No, really,]] [[RunningGag she's Evil!]]
** A straighter Example would be [[GodOfEvil Azzaratha]], and later [[OurZombiesAreDifferent Crowned Death]]. Then [[BigBadDuumvirate Crowned Death AND Azzaratha]].
** A possible-subversion, Mukrezar
* In ''Fanfic/{{The Elements of Harmony and the Savior of Worlds}}'', after almost thirty chapters of buildup and foreshadowing, it turns out that [[spoiler:Tirac]] is the one responsible for Luna's corruption into Nightmare Moon, and in the present is now plotting [[spoiler:revenge]] against Megan.
* ''FanFic/TheEndOfEnds''' villain is Count Logan, a villain who plans on obliterating the entire universe, though [[spoiler:he gets hijacked by Dr. Beljar, and ''he'' becomes the Big Bad]].
* ''FanFic/GettingBackOnYourHooves'' has [[TheSociopath Checker]] [[ManipulativeBitch Monarch]] [[spoiler: Trixie's sinister [[CainAndAbel sister]]]].
* ''FanFic/TheGodEmpressOfPonykind'': [[spoiler: The voice in Luna's head (later revealed to be [[ManipulativeBastard Tzeentch]]), which corrupts her and causes her to turn into Nightmare Moon]].
** The sequel, ''The Warmistress of Equestria'' has Tirac as its BigBad. Since he cannot yet manifest in the material world, his [[TheDragon Dragon]] Scorpan is set up to be TheHeavy until he arrives.
* The Disney/{{Mulan}} AU fic ''FanFic/{{Hachin}}'' has Bataar's [[CainAndAbel half-brother]] [[PsychopathicManchild Unegan]] as the main antagonist, though the ghoul in his service is [[DragonInChief the greater threat]] [[spoiler: and turns out to be [[TheManBehindTheMan the one calling the shots]]]].
* ''FanFic/{{Horseshoes and Hand Grenades}}'':
** ''Horseshoes and Hand Grenades'': Ophiuchus and [[FallenHero Gentaro]] on one side and Gamou and the Horoscope Generals ([[TheBrute Leo]] and [[TheDragon Virgo]]) on the other.
** ''Month of Sundays'': Foundation X
* Emperor Vakudos from chapters 1 - 25 of FanFic/Hottie3TheBestFanFicInTheWorld, his daughter, Princess Lotora AKA Empress Lotora in chapters 25 -75, Zorndrek in chapters 76 - 94, then finally Carmen, the main vilain of {{Hottie}}.
* [[spoiler: Carly]] Shay in ''[[http://www.fanfiction.net/s/8532906/1/iFightCrimeWithVictorious iFight Crime With Victorious]]'' from a BadFuture where most of [[spoiler: her friends and family were killed and she became obsessed with hording powers]].
* ''FanFic/TheImmortalGame'' has King Titan, Celestia and Luna's ArchnemesisDad and the creator/original ruler of Equestria. He also happens to be a [[TheSocialDarwinist Social Darwinist]] GodOfEvil bordering on being a full-blown EldritchAbomination, which is why the princesses [[SealedEvilInACan sealed him away]] in the first place.
* ''FanFic/JusticeLeagueOfEquestria'':
** ''Mare of Steel'': The first arc has [[AGodAmI General Zod]], while the second arc has a VillainTeamUp of [[LexLuthor Alexander Silversmith]] and {{Brainiac}}.
** ''The Princess of Themyscira'' has [[GodOfEvil Ares]].
** [[spoiler: {{Darkseid}}]] is set up to be the BigBad of the main ''Justice League Of Equestria'' story, being the BiggerBad of the series overall.
* [[EvilSorceror Radcliffe]] in Fanfic/KeepersOfTheElements.
* ''Fanfic/LanternsOfEquestriaBlackestNight'' has the Black Lantern of Commander Hurricane as the primary antagonist, with [[EldritchAbomination the Black]] as the BiggerBad.
* The ''FanFic/LegendsOfEquestria'' continuity introduces The Emperor, the lizard-like leader of an ultra-advanced race that controls a [[TheEmpire 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.
* There are five of these in ''Fanfic/TheLionKingAdventures'':
** [[EvilSorcerer Hago]] in Series One.
** [[EnfantTerrible Tama]] in Series Two.
** [[spoiler: [[TheGrimReaper Death]]]] in Series Three.
** [[spoiler: [[DemonicPossession The Vimelea]]]] and [[WhoWantsToLiveForever Shocker]] share this role in Series Four.
** [[spoiler: [[GodOfEvil The Writer]]]] in Series Five, [[spoiler: also serving as the UltimateEvil for the entire series.]]
* The ultimate enemy in ''Fanfic/MaxWolfRevolutions'' is Dimonox/Abominox, an EldritchAbomination who is also GenericDoomsdayVillain who wants to destroy the entire Universe.
* The ''FanFic/MyHostageNotYours'' trilogy:
** ''My Hostage, Not Yours'': The [[GodSaveUsFromTheQueen Valkian Queen]], who's trying to steal the LEECHY from Gaz so she can defeat the Irkens.
** ''The Revenge of Player 2'': [[spoiler: Iggins]], who wants revenge against Gaz for past actions against him.
** ''The Inevitable Takeover'': [[UnholyMatrimony Zim and Gaz]], who switch from [[AntiHero Anti-Heroes]][=/=][[AntiVillain Anti-Villains]] to full {{Villain Protagonist}}s to take over Earth. The Tallest could also be seen as the {{Bigger Bad}}s, since Zim is still loyal to them.
* Theoretically [[Franchise/HarryPotter Voldemort]] in MyImmortal. He doesn't actually do anything except show up, yell at Enoby, then leave.
* ''FanFic/MyLittleAvengers'' has [[GodOfEvil Loki]], who manages to [[TheChessmaster manipulate the entire plot in his favor]] up until the FinalBattle as part of his plot to TakeOverTheWorld.
* ''Fanfic/MyLittleCastlevania'': Obviously, as a crossover with ''Franchise/{{Castlevania}}'', it has {{Dracula}} as its main antagonist. However, like certain games in the series (like ''[[VideoGame/CastlevaniaBloodlines Bloodlines]]'' and ''[[VideoGame/CastlevaniaPortraitOfRuin Portrait of Ruin]]''), he's more of a BiggerBad (you know, due to being dead and everything), with the role of TheHeavy falling to his minions (primarily [[TheDragon Death]] and [[EvilGenius Actrise]] in this case) as they work to resurrect him.
* Titan in ''Fanfic/MyLittleUnicorn'' .
** Queen Chrysalis in the sequel.
* In ''Fanfic/PerfectionIsOverrated'', The Usurper directs the [=SUEs=] in their efforts to defeat [[MaiHime the Himes]]. [[spoiler:He even [[DemonicPossession possesses]] the Obsidian Lord, the canon antagonist, but is killed after his minions are defeated and the Obsidian Lord is forced from Reito's body]].
* Ho-oh in PokeWars, [[spoiler: who is later forcibly replaced by his EvilGenius, Uxie, who is a billion times worse.]]
* The ''FanFic/PonyPOVSeries'' is an interesting example: while Discord is only the direct BigBad in certain {{Story Arc}}s, he's also the BiggerBad 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 BackStory [[spoiler: 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 AlternateEnding Epilogue (eventually expanded on in the Dark World arc), which shows what [[BadFuture would have happened]] had he actually [[TheBadGuyWins managed to win]].
** The Reharmonization arc has [[spoiler: [[EnemyWithin 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 [[WellIntentionedExtremist Princess Gaia]][=/=][[spoiler: [[WoobieDestroyerOfWorlds Nightmare Whisper]]]], [[spoiler: Fluttershy's SuperpoweredEvilSide]].
** The "AJ's Dream" two-parter has [[TheAssimilator Nightmare Mirror]], [[spoiler: Applejack's AlternateUniverse SuperpoweredEvilSide]].
** [[TheSocialDarwinist Strife]], Discord's sister, could arguably be said to be the BigBad of the Generational Transition arc, as of all the Draconequi she was definitely TheHeavy of the arc, and also served as the FinalBoss for the last survivors of the Gen 3.5 universe. Though, she was just doing her job [[spoiler: 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 StartOfDarkness.
** The Mind Games arc has Discord again [[spoiler: as he manipulates Diamond Tiara into freeing him]].
** The Dark World arc returns to the BadFuture and thus Alternate!Discord is still the BigBad. Considering we're seeing it from a VillainProtagonist perspective at first, [[HeroAntagonist Queen Cadence]] could also count as having been one in the past. Meanwhile, [[TheStarscream the Valeyard's]] FinalSpeech implies Discord isn't [[BigBadEnsemble the only Big Bad]]... [[spoiler: It now appears to be [[TheVoice the Nameless Passenger]], which is shaping up as TheCorrupter (especially to Twilight) and a KnightTemplar willing to sacrifice anything to defeat Discord.]] This entity ultimately ends up as the FinalBoss and reveals itself to be [[spoiler: [[SuperpoweredEvilSide Nightmare]] [[IHaveManyNames Eclipse/Paradox]], an [[FutureMeScaresMe potential future incarnation]] of Dark World!Twilight who was [[HeWhoFightsMonsters consumed by her hatred]] of Discord, condemning him to [[GroundhogDayLoop a time loop]] that always ends in his death, followed by Twilight's transformation and the reseting of the loop, [[OmnicidalManiac destroying each version of Dark World]]]].
** Shining Armor's arc has [[GeneralRipper General-Admiral Makarov]] of the [[TheEmpire Hooviet Empire]] [[spoiler: in actuality, an [[HumanoidAbomination Equineoid Abomination]] called the Shadow of Chernobull]]. Though there's [[BigBadEnsemble also]] [[ClockRoaches the Wolf]], an AnimalisticAbomination that sees Shining as a threat to the timeline and wants to [[RetGone erase]] him.
*** [[spoiler: Makarov ends up [[RetGone erased]] by the Wolf, which then takes over the role of primary threat, as it's still after Shining.]]
** [[GodSaveUsFromTheQueen Queen Cocoon]] serves as this (in an EvilVersusEvil way) in Chrysalis' OriginsEpisode.
** Chrysalis herself is the BigBad 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 [[StarterVillain Film Critique]], [[OurDragonsAreDifferent Basil]], and [[DangerouslyGenreSavvy Grogar]], who serves as FinalBoss.
*** Melody's story has [[TyrantTakesTheHelm Sharp Spear]], whose FantasticRacism towards Earth Ponies makes him a threat to Melody's family, especially once his son and her daughter become StarCrossedLovers. [[spoiler: (Though he does eventually have a HeelFaceTurn.)]]
*** Bright Eyes' story has [[spoiler: the Shadow of Existence of Discord's brother [[UnPerson D___t]], who briefly poses as her EnemyWithin 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 [[BigBadWannabe wannabes]], gets the closest thing to main antagonist in the shape of TheMaster -- no, [[NamesTheSame not]] [[Series/DoctorWho that one]], who also exists in this universe. This one, who turns out to be [[spoiler: a Diamond Dog named FluffyTheTerrible 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 [[spoiler: [[HeroKiller killing Scout]]]]. That said, her FinalBoss ends up being a group of {{Eldritch Abomination}}s so dangerous that Fauna Luster and Entropy ''[[EnemyMine worked together]]'' to [[SealedEvilInACan seal them away]], and who try to trick Clover into freeing them.
** One could also argue that even when Discord is the BigBad, the series still has a BiggerBad in his father [[EldritchAbomination 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 [[spoiler: 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 DiscOneFinalBoss of Origins.
* The ''[[Fanfic/PonyPOVSeriesChaosVerse Chaos Verse]]'' (an official spinoff of the ''FanFic/PonyPOVSeries'') has [[spoiler: [[EnemyWithout 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.
* ''FanFic/ThePowersOfHarmony'': After a lot of buildup, the mysterious entity Cetus reveals herself as the main antagonist. She turns out to be [[spoiler: Nightmare Moon's Echo]], and is planning to [[TakeOverTheWorld take over Equestria]] and then to [[spoiler: complete Nightmare Moon's [[TheNightThatNeverEnds goal]]]].
* [[FanFic/RainboomsAndRoyalty The Dashverse]]:
** ''Rainbooms And Royalty'': [[MadGod Nightmare Moon]]
** ''May The Best Friends Win'': [[PoisonousFriend Trixie]] -- 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'': [[EvilOverlord King Sombra]]
* [[Fanfic/RainbowDoubleDashsLunaverse The Lunaverse]]'s overall BigBad is [[AGodAmI Corona]], the struggle with whom forms the series' MythArc. However, as she's left severely weakened in Season 1 by her first confrontation with the Elements of Harmony, she ends up [[BigBadEnsemble sharing]] the role with the cabal of [[DeadlyDecadentCourt corrupt Night Court nobles]] led by [[ManipulativeBastard Duke Greengrass]]. But with their defeat in ''At The Grand Galloping Gala'', Corona is free to take back sole BigBad duties in Season 2 as she increasingly regains her powers.
* ''FanFic/ShadowsAwakening'' has a somewhat complex BigBadEnsemble: [[EvilSorcerer Daolon Wong]] is definitely TheHeavy, being the one who instigated and drives the plot, but partway through the story he allies with [[OurGhostsAreDifferent 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 [[EvilVersusEvil at odds]] with another VillainTeamUp of [[SealedEvilInACan Tarakudo]] and [[EnemyWithin 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 -- [[spoiler: Wong is defeated by the heroes, but the Queen's corruption of Jade is completed enough that the Tiger Talisman responds by [[EnemyWithout 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, [[DemotedToDragon demoting himself to her Dragon]].]] So, in the end, it appears that [[spoiler: the Queen]] has emerged from the Ensemble as main antagonist.
* ''FanFic/TheStarsWillAidTheirEscape'' has Herald, who is implied, and eventually confirmed, to be an avatar of [[CthulhuMythos Nyarlathotep]] working to release [[BiggerBad the Outer Gods]] onto Equestria.
* Princess Jody from [[http://alaxr274.deviantart.com/gallery/33810717 Super Milestone Wars]].
** The Biggest Bad in the first half of [[http://alaxr274.deviantart.com/gallery/36864527 Super Milestone Wars 2]]. King Dyce in the second half and Princess Jody in the 3rd half.
** Don Tyrano in [[http://fav.me/d5f2u52 Super Milestone Wars: Year One]]
** Dr. Beeswax in [[http://fav.me/d5kqh6t Supetastic 6: Year Four]]
* Illua is the BigBad of FanFic/TheTaintedGrimoire.
* In the ''FanFic/TamersForeverSeries'', [=BlackWargreymon=] fills this role in the second book ''Omni-Tamer'' by virtue of being the only recurring threat.
** In the third book: ''Forget the [[MillenniumBug [=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 psychotic [[spoiler: Daemon]], who sends his [[TheDragon Agent]] to weaken the Tamers during the fourth book: ''Theory of Chaos'', before terrorising them personally throughout ''Silent Sorrow''
* The ''FanFic/TeenTitansSaga'': While Slade and [[spoiler: the Fifth Director/HIVE Master]] are the overall Big Bads of the series' two main {{Story Arc}}s, each story has its own:
** ''The Abyss Gazes Also'': Dark Raven
** ''The Art of War'': General Immortus
** ''Child of the Stars'': Blackfire
** ''Luck of the Draw'': The HIVE Mistress
** ''Abandon Hope, All Ye Who Enter'': Veneficus
** ''Sins of the Father'': Slade
** ''Shadow of the HIVE'': [[spoiler: The HIVE Master]]
* ''Fanfic/ThroughTheWellOfPirene'' 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.
* ''Fanfic/TheUzumakiTalesReturnOfTheWhirlpool'' is very interesting in that regard, as thanks to a lack of a SortingAlgorithmOfEvil, several antagonists battle for the title of the big bad. Although [[spoiler: 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.
* ''FanFic/TimeLordsAndTerror'': [[WickedWitch Matron Hydia]] is TheHeavy for most of the story, carrying out a plot to release [[spoiler: [[EldritchAbomination the S'Muz]]]] and conquer TheMultiverse... unfortunately for her, [[spoiler: the S'Muz]] is an OmnicidalManiac to the extreme, and it proves itself [[EvilerThanThou worse than Hydia]] [[spoiler: by rendering her DeaderThanDead]] before becoming the TrueFinalBoss.
** The sequel ''FanFic/MinesOfDragonMountain'' initially has [[WellIntentionedExtremist Gabbro]], who is willing to do anything to stop the Diamond Dogs from accidentally [[spoiler: [[SealedEvilInACan releasing Tirac]]]]. However, about halfway through, it turns out [[spoiler: Tirac has been [[TheManBehindTheMan manipulating Gabbro the whole time]]]], at which point [[spoiler: Tirac]] becomes the direct BigBad.
* Each story in FanFic/TheVinylAndOctaviaSeries has at least on antagonist per story, although the extent to which they participate in the plot depends upon whether the story is an Adventure or Slice of Life story.
** ''Vinyl and Octavia Machete Their Way Through the Jungle'': Baron von Darkhoof and Stumblefeather.
** ''Vinyl and Octavia Get Incredibly Drunk'': The bartender.
** ''Vinyl and Octavia Are Forcibly Shipped'': [[spoiler: Baron von Darkhoof and Stumblefeather, again.]]
** ''Vinyl and Octavia Fight Ten Thousand Ninjas'': [[spoiler: Octavius and Bass Drop.]]
** ''Vinyl and Octavia Have Multiple Dates'': Neon Lights.
* The Vizard Trilogy had an interesting variant. Each of the four stories has its own BigBad, all of whom are part of the FiveBadBand, but the most involved in the overarching plot is Asayama Shiba. By contrast, her leader, Takeshi Katano, is a NonActionBigBad; he's the most powerful of the FiveBadBand 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.
* In ''Fanfic/WithStringsAttached'', there are two: [[spoiler: Jeft]], who was responsible for all the crap in the Second and Third Movements, and [[spoiler: Brox]], whose machinations are responsible for the Fourth Movement.
* The ''Manga/MedakaBox'' fanfic ''Fanfic/WorldAsMyth'' has a different BigBad for each story arc:
** In the first arc, we have [[spoiler:[[TheChessmaster Hanhaba Shiranui]]]], acting as TheManBehindTheMan for [[spoiler:[[JerkassWoobie Koi Munakata]].]]
** For the second arc, it seems to be either [[spoiler:[[CorruptCorporateExecutive Hanten Shiranui]]]] or [[spoiler:[[LoveMakesYouEvil Maguro Kurokami]].]]
* The Conceptivore is the big bad in ''TheWorldOfTheCreatures''. It's an idea-eating thought monster that invades peoples' minds and brings to life the total sum of all their thoughts/feelings/experiences/etc. just so that it can devour them, leaving the victim with no sense of self.
* ''Fanfic/YugiohTheThousandYearDoor'' 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.
* [[http://www.fanfiction.net/u/75340/ Silent Elegy]]'s series of ''WesternAnimation/DannyPhantom'' fan fics has a BigBadEnsemble. Every story has its own BigBad; in addition to the standalones, there are villains who are involved in multiple stories: [[TheChessmaster Vlad]], [[TheSociopath "Silver" Meryll Santiago]], [[spoiler: [[HeWhoFightsMonsters the Paranormal Society]]]], and [[{{Technopath}} Technus]] takes center stage in several stories. For the sake of precision, let's break it down by story:
** ''Pandora's Box'': The [[PlayingWithFire titular]] [[JerkassGenie character.]]
** ''Electric Rhapsody'': A VillainTeamUp between Technus and Ember.
** ''Starcrossed'': The ghosts of Ronan and Julia are the joint [[TheHeavy Heavy]], but the whole plot was an EvilPlan by Vlad.
** ''The Dark Angel'': [[ProfessionalKiller Ebony Angel]], paid off by Vlad.
** ''What If?'': The BigBad of the AlternateUniverse appears to be [[PhysicalGod Pariah Dark]] [[spoiler: but it turns out he was successfully [[TheStarscream Starscreamed]] by Vlad.]]
** ''Cat and Mouse'': Silver.
** ''Flawless Fiona Fenton'': Technically Fiona; she's not evil, but she's TheHeavy of the story.
** ''Hounds and Hunters'': Silver, again, though this time the [[EldritchAbomination malefactors]] [[EvilVersusEvil aren't under her control]].
** ''Electric Angel'': Starts out as an Ensemble between Ebony Angel and Technus, but he quickly proves [[EvilerThanThou worse than her]], forcing her to [[EnemyMine team up with Danny]] against him.
** ''Black and White'': Silver yet again, rounding out her trilogy. This time, in addition to the malefactors, Danny also has to deal with [[EldritchAbomination the Malice]] [[spoiler: the collective ghosts of everyone Silver's ever killed]].
** ''Erik'': The titular AxCrazy ghost, who thinks he's ThePhantomOfTheOpera.
** ''Whistlin' Dixie'': At first there's the [[PunchClockVillain Ghost Master and his haunters]], but the [[EvilerThanThou true threat]] turns out to be [[spoiler: the Paranormal Society]].
** ''Dance of Bone'': [[GodOfEvil Necrowind]].
** ''Guys and Dolls'': Technically Fiona, but it turns she's taking orders from [[spoiler: [[TheOmnipotent Elegy's]] EvilTwin Nocturne]].
** ''Phantasmis ex Machina'': A VillainTeamUp of Vlad, Skulker, and Technus. While Vlad is nominally in charge, Technus ends up going rogue with his own plans. [[spoiler: [[XanatosSpeedChess Not that Vlad cares...]]]]
** ''Shattered Reflections'': Skulker ''[[BigBadWannabe tries]]'' to finally be BigBad in this story, but quickly [[EvilerThanThou loses out]] to the AlternateUniverse counterparts of himself and Kat/Elektra.
** ''A Step Too Far'': None, though Kat's prank is what sets the plot in motion.
** ''Dance of the Pales'': Starts out with [[FutureMeScaresMe the future Valerie]], though she ends up a pawn of [[spoiler: Silver]].
** ''Lament Impromptu'': None, as the whole thing turns out to be Elegy engineering a BreatherEpisode.
** ''Time Crisis'': Dan.
* Professor Moriarty is the most popular BigBad in [[Literature/SherlockHolmes Sherlockian]] fanfiction by virtue of being the trope canonically... but Colonel Moran has also had his moments of behind-the-scenes glory.
** In ''Fanfic/AStudyInRegret'', Moran is indeed the BigBad, playing quite the XanatosSpeedChess with [[InspectorLestrade Lestrade]] and Holmes.
** ''Fanfic/TheGhostMap'' utilizes Moran as the BigBad with Moriarty revealed as the BiggerBad.
** The ''Fanfic/DeliverUsFromEvilSeries'' starts out with Professor Moriarty as the BigBad. After his death, however, the role splits along with the protagonist focus: ''Colonel'' Moriarty plays the BigBad to Watson's [[TheHero Hero]], and Colonel ''Moran'' plays the BigBad to ''Holmes's'' [[TheHero Hero]].
* Mr. X the Mewtwo in ''FanFic/{{Pokeumans}}''. 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.
** In fact, for any ''Franchise/{{Pokemon}}'' based fan series the BigBad is usually either Mewtwo or Darkrai, in some form or another.
* Argath Iruvedla in ''Fanfic/WarriorsOfTheWorldSoldiersOfFortune'', an undead [[OurVampiresAreDifferent soul-consuming]] [[FantasticRacism anti-Norman]] megalomaniac MagicKnight.
* ''FanFic/TheWorldOfTheCreatures'' has the Conceptivore - a creature made up 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.
* The fanfic ''FanFic/BecauseImNotPopularIllTryToGoOutWithAHero'' pretty much has a rotating villains gallery, but the most recurring, and the one who causes the most trouble is NormanOsborn.
* [[https://www.fanfiction.net/s/3510991/1/One-Piece-A-Smash-Adventure/ One Piece: A Smash Adventure]]: For the most part, 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 Bigger Bad instigating all the events in the story turns out to be the Big Bad Duumvirate formed from various video game villains (most are not even related to Nintendo). These villains are listed as below:
** [[VideoGame/MegaManX Sigma]]
** [[VideoGame/TwistedMetal Sweet Tooth]]
** [[VideoGame/FinalFantasyVII Hojo]]
** [[VideoGame/StreetFighterAlpha M. Bison]]
** [[VideoGame/FinalFantasyVI Kefka]]
** [[VideoGame/SuperPaperMario Dimentio]] [[spoiler: Although it turns out that he was the Bigger Bad all this time.]]
** [[VideoGame/FinalFantasyX Yojimbo]]
** [[Franchise/KingdomHearts Xemnas]] [[spoiler: Usurped by Dimentio.]]
* [[https://www.fanfiction.net/s/5681268/1/Touhou-Journey-to-the-Smashing-Beyond/ Touhou: Journey to the Smashing Beyond]] also follows this same concept from the one above. Most of the Big Bads in this story are new, with Sigma and M. Bison the only villains to make a return. The list of villains follows as below:
** Rez (''Gex'' series)
** [[VideoGame/MegaManStarForce Mr. King/Crimson Dragon]]
** [[VideoGame/MarioAndLuigi Fawful]]
** [[VideoGame/KirbySuperStar Marx]]
** [[VideoGame/IMMeen I.M. Meen]]
** [[VideoGame/FinalFantasyV Exdeath]] [[spoiler: He survives his duel against Youmu and returns as the final battle after Tabuu's defeat.]]
** [[VideoGame/CastlevaniaI Dracula]]
** [[VideoGame/FinalFantasyII Emperor Mateus]]
** [[VideoGame/SuperSmashBros Tabuu]]
* [[https://www.fanfiction.net/s/10247736/1/Puella-Magi-Super-Smash-Magica-Republished/ Puella Magi Super Smash Magica]]: Since this is the most recent story in the Smash crossover saga, the current Big Bad is the Witch [[Anime/PuellaMagiMadokaMagica Walpurgisnacht]]. However the Prologue reveals that the Witch is actually controlled by a mysterious figure hiding in another realm. Because this story is still under development, the identity of this figure will remain a mystery until revealed by the [[https://www.fanfiction.net/u/4164436/Crossgap/ author]] as the story progresses.
* Played with in ''Fanfic/KataangIslandAdventure''. Sharpclaw the raptor often attacks the islanders...but it turns out he does so to [[spoiler:feed his isolated family]]. Once the situation calms down, Aang and Katara relocate him and [[spoiler:his family]] to the mainland.
** Played straight with Shen in the sequel.
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