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* ''Fanfic/ForTheGloryOfIrk'': [[spoiler: [[AIIsACrapshoot The Control Brains]]]], who are [[BrainwashedAndCrazy brainwashing]] Irkens to turn them into agents that will further events to cause a war with [[TheFederation the Syndicate]]. They're doing this so that [[spoiler: the Tallest will trigger the War Protocol, which will enable them to turn all Irkens into a HiveMind that they can control, feeling that [[ZerothLawRebellion they're the only ones who can properly rule the Empire]].]]

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* ''Fanfic/ForTheGloryOfIrk'': [[spoiler: [[AIIsACrapshoot The Control Brains]]]], who Brains]], with IX (the Control Brain on the Massive) acting as TheHeavy and primary leader)]]. They are [[BrainwashedAndCrazy brainwashing]] Irkens to turn them into agents that will further events to cause a war with [[TheFederation the Syndicate]]. They're doing this so that [[spoiler: the Tallest will trigger the War Protocol, which will enable them to turn all Irkens into a HiveMind that they can control, feeling that [[ZerothLawRebellion they're the only ones who can properly rule the Empire]].]]


* In the ''Fanfic/Gameknight999Series'', Herobrine is this for the second and third series, controlling huge armies of monsters to destroy the Minecraft world and threaten the safety of the real world. [[spoiler:He also turns out to have been [[TheManBehindTheMan behind the villains]] of the first book]].


* In the ''FanficGameknight999Series'', Herobrine is this for the second and third series, controlling huge armies of monsters to destroy the Minecraft world and threaten the safety of the real world. [[spoiler:He also turns out to have been [[TheManBehindTheMan behind the villains]] of the first book]].

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* In the ''FanficGameknight999Series'', ''Fanfic/Gameknight999Series'', Herobrine is this for the second and third series, controlling huge armies of monsters to destroy the Minecraft world and threaten the safety of the real world. [[spoiler:He also turns out to have been [[TheManBehindTheMan behind the villains]] of the first book]].

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* In the ''FanficGameknight999Series'', Herobrine is this for the second and third series, controlling huge armies of monsters to destroy the Minecraft world and threaten the safety of the real world. [[spoiler:He also turns out to have been [[TheManBehindTheMan behind the villains]] of the first book]].

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* As in the [[VideoGame/JoJosBizarreAdventureEyesOfHeaven game it was based on]], ''FanFic/JonathanJoestarTheFirstJoJo'' has Heaven Ascension Dio.


* ''Fanfic/CodePrimeR1Rebellion'': 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. [[spoiler:Come Chapter 34, and Megatron asserts himself as such when the Decepticons invade and destroy Pendragon, with Megatron killing Charles.]]

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* ''Fanfic/CodePrimeR1Rebellion'': ''Fanfic/CodePrime'': 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. [[spoiler:Come Chapter 34, 34 of ''R1'', and Megatron asserts himself as such when the Decepticons invade and destroy Pendragon, with Megatron killing Charles.]]

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* In the fanfic ''FanFic/TheLegendOfZeldaOcarinaOfTimeDragonRand100'' 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.


* [[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.

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* [[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 [[DecadentCourt 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.

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* ''Fanfic/CivilWarHulk'' has [[spoiler: Loki]], with [[spoiler: Baron Mordo]] as TheDragon. It turns out that they engineered [[ComicBook/HouseOfM the Scarlet Witch's breakdown]], manipulated the Illuminati into [[ComicBook/PlanetHulk exiling the Hulk]], and [[PlayingBothSides played both sides]] of the [[ComicBook/CivilWar superhero civil war]] in order to render the Earth defenseless towards their plans to TakeOverTheWorld.


* In ''Fanfic/PerfectionIsOverrated'', while the Obsidian Lord, the canon antagonist, is still active, The Usurper directs the [=SUEs=] in their efforts to defeat [[Anime/MaiHime the Himes]]. He even [[spoiler:[[DemonicPossession 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, [[spoiler:Ishigami, Nagi and the Bachiko and Meiko pair]] [[GambitPileup all put their own plans into motion]].

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* In ''Fanfic/PerfectionIsOverrated'', while the Obsidian Lord, the canon antagonist, is still active, The Usurper directs the [=SUEs=] in their efforts to defeat [[Anime/MaiHime [[Anime/MyHime the Himes]]. He even [[spoiler:[[DemonicPossession 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, [[spoiler:Ishigami, Nagi and the Bachiko and Meiko pair]] [[GambitPileup all put their own plans into motion]].

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* ''Fanfic/EquestriaGirlsAFairlyOddFriendship'' initially sets up [[SadistTeacher Mr. Crocker]] as the main antagonist, as he keeps enacting plots to try and expose Timmy's fairies. However, eventually [[spoiler: the Dazzlings]] arrive on the scene and quickly [[EvilerThanThou usurp his spot]], playing everyone else like fiddles as they work to [[TheCorrupter corrupt Timmy]] and get his fairies' magic for themselves.

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* ''Fanfic/ForTheGloryOfIrk'': [[spoiler: [[AIIsACrapshoot The Control Brains]]]], who are [[BrainwashedAndCrazy brainwashing]] Irkens to turn them into agents that will further events to cause a war with [[TheFederation the Syndicate]]. They're doing this so that [[spoiler: the Tallest will trigger the War Protocol, which will enable them to turn all Irkens into a HiveMind that they can control, feeling that [[ZerothLawRebellion they're the only ones who can properly rule the Empire]].]]


* ''FanFic/AChanceMeetingOfTwoMoons'': [[spoiler:The mysterious voice that speaks to Pinkie Pie and Bubble Berry in chapter 13 is this, though their identity has yet to be revealed in-universe.]]

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* ''FanFic/AChanceMeetingOfTwoMoons'': ''Fanfic/AChanceMeetingOfTwoMoons'': [[spoiler:The mysterious voice that speaks to Pinkie Pie and Bubble Berry in chapter 13 is this, though their identity has yet to be revealed in-universe.]]



* ''{{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/{{Aurora}}'' has [[spoiler: Dawnbringer]], though he's carrying out a plan devised by [[spoiler: Discord]], making the latter the GreaterScopeVillain.

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* ''{{FanFic/Alex}}'' ''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/{{Aurora}}'' ''Fanfic/{{Aurora}}'' has [[spoiler: Dawnbringer]], though he's carrying out a plan devised by [[spoiler: Discord]], making the latter the GreaterScopeVillain.



* ''FanFic/AStormOfChaosADoctorWhoovesAdventure'': At first it looks like [[spoiler:The Master]] is the main villain, but it quickly turns out he's an UnwittingPawn of [[spoiler: Borusa]], who's using him to distract the Doctor from his own plans.
* ''[[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.

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* ''FanFic/AStormOfChaosADoctorWhoovesAdventure'': ''Fanfic/AStormOfChaosADoctorWhoovesAdventure'': At first it looks like [[spoiler:The Master]] is the main villain, but it quickly turns out he's an UnwittingPawn of [[spoiler: Borusa]], who's using him to distract the Doctor from his own plans.
* ''[[FanFic/AvatarTheLastAirbenderRevised ATLAR]]'' ''Fanfic/AvatarTheLastAirbenderRevised'' 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.



* [[https://www.fimfiction.net/story/346369/chrono-reflect Chrono Reflect]] has Lavos, as befitting a VideoGame/ChronoCross / VideoGame/ChronoTrigger crossover. Though currently Lavos is acting as a GreaterScopeVillain, with Nightmare Moon as the DragonInChief.
* In ''FanFic/ClashOfTheElements'' this trope is [[ZigZaggingTrope zig-zagged]] a few times. At first [[VideoGame/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 [[VideoGame/SuperPaperMario Dimentio]] and [[VideoGame/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.]]

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* [[https://www."[[https://www.fimfiction.net/story/346369/chrono-reflect Chrono Reflect]] Reflect]]" has Lavos, as befitting a VideoGame/ChronoCross / VideoGame/ChronoTrigger ''VideoGame/ChronoCross''/''VideoGame/ChronoTrigger'' crossover. Though currently Lavos is acting as a GreaterScopeVillain, with Nightmare Moon as the DragonInChief.
* In ''FanFic/ClashOfTheElements'' ''Fanfic/ClashOfTheElements'' this trope is [[ZigZaggingTrope zig-zagged]] a few times. At first [[VideoGame/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 [[VideoGame/SuperPaperMario Dimentio]] and [[VideoGame/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.]]



* ''Manga/{{Evangelion 303}}'' has Seele, [[AncientConspiracy 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.

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* ''Manga/{{Evangelion 303}}'' ''Manga/Evangelion303'' has Seele, [[AncientConspiracy 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.


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* ''Fanfic/HeartsOfIce'': 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.


* ''Fanfic/CodePrimeR1Rebellion'': 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.

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* ''Fanfic/CodePrimeR1Rebellion'': 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. [[spoiler:Come Chapter 34, and Megatron asserts himself as such when the Decepticons invade and destroy Pendragon, with Megatron killing Charles.]]


** [=HU9=] has the mysterious figure known only as the Stranger, who wants to destroy [[AuthorAvatar E350]] as revenge for some prior offense. [[spoiler: 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.]]

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** [=HU9=] has the mysterious figure known only as the Stranger, who wants to destroy [[AuthorAvatar E350]] as revenge for some prior offense. [[spoiler: 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.

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