History Main / WrongSideAllAlong

-->-- '''Never Existed''', ''Music/{{Keldian}}''

Subtrope of EvilRunningGood; this is specific in that the antagonist is (also) a good guy (while that trope can have actual bad guys as antagonists). Compare UnwittingPawn and HeelRealization.

* ''Anime/{{Daimos}}'': [[AlienPrince Richter]] spent most of the series despising humans and riding up the death toll to the millions for killing his father and dooming his people as refugees. Though he later finds out that it was a fellow [[AngelicAliens Baam]] who killed him, his hatred for humans is not shaken, and he states he won't be satisfied until he cleanses the Earth and replaces them. Kazuya proves that his [[HumansAreBastards views]] are wrong by putting his body through relentless abuse and torture just to get a small chance at saving the refugees in Baam cryostatis. It is then that Richter's entire worldview changes - a mere human like Kazuya, doing his best to help him while being covered in scars (while the Baam King Olban abandoned them) makes him realize why his sister fell in love with the humans.

* ''Literature/TheHeroLaughsWhileWalkingThePathOfVengeanceASecondTime'' is about a FallenHero and his party of the Betrayed using his time-travel fueled second chance to take revenge on a CrapsaccharineWorld which conned him into thinking he was in a stereotypical fantasy game, only to reveal at the very end that his side was composed of genocidal psychopaths who pinned the blame for their mass-murders of innocents on him.
* ''Literature/MushokuTenseiJoblessReincarnation'': Early on in his reincarnation, Rudeus begins receiving visions from an enigmatic being calling himself Hitogami who provides cryptic advice to him. Later on, he crosses paths with Hitogami's ArchEnemy Orsted who ends up punching a hole in Rudeus's chest upon learning that he knows of Hitogami. Naturally, this leads Rudeus to be incredibly fearful of Orsted and thus more trusting of Hitogami. However, Rudeus eventually encounters a future version of himself who reveals to him that Hitogami is EvilAllAlong, and that in the BadFuture he came from he lost everyone he cared for thanks to him falling for Hitogami's manipulations.

* In the third ''Anime/RebuildOfEvangelion'' movie, poor Shinji falls victim to two instances of this: Just after having left the RenegadeSplinterFaction of the organization he used to work for, he finds out that said organization, ''including his own father Gendo'', has been plotting doomsday for quite a while, and, in fact, successfully [[NiceJobBreakingItHero set him up to cause it]] ''for them'' in a futile attempt to save his LoveInterest, and, in fact, brought the two of them together for that exact purpose. Then, he gets told that he can fix the now nigh-inhabitable planet by obtaining a certain ArtifactOfDoom, which he sets out to get, having to [[WeUsedToBeFriends fight his former roommate and friend Asuka]] in the process. When he actually gets his hands on the artifacts, they do, [[UnwittingPawn obviously]], cause yet another near-apocalypse as Shinji [[MyGodWhatHaveIDone stares in horror]].

[[folder:Films - Animation]]
* At first it's not clear that ''WesternAnimation/AtlantisTheLostEmpire'' even has an [[NoAntagonist antagonist]]. Then Milo finds out that the rest of the crew led by Rourke are actually mercenaries out to steal Atlantis' PowerCrystal so they can sell it to the highest bidder, and are (at first) willing to doom the Atlanteans in the process. Fortunately, all of them but [[BigBad Rourke]] and Helga (and their small army of mooks) make a HeelFaceTurn.

[[folder:Films - Live Action]]

* ''Film/IndianaJonesAndTheLastCrusade''. Indiana Jones fights against the Brotherhood of the Cruciform Sword during the film. It turns out they're just trying to protect the Grail's hiding place from the Nazis. The person who sent Jones on the mission to find the Grail, Walter Donovan, is really the Big Bad and a Nazi sympathizer [[FriendToPsychos (well, kind of)]].

* In ''Film/{{Wanted}}'', the protagonist is brought into [[AncientTradition the Fraternity]], a killer organization (with TheMentor, TheLancer, etc.), to [[YouKilledMyFather kill the man who killed his father]]. It's eventually revealed that [[LukeIAmYourFather the bad guy is really his father]] and he was trying to stop the organization, which is shown to be corrupted. Cue HeelRealization and StormingTheCastle.

* ''Series/Fallout2024''; Lucy [=MacLean=] sets out from Vault 33 in pursuit of Lee Moldaver, a raider chieftain who broke into her Vault and kidnapped her father Hank for nefarious purposes. But as it turns out, [[spoiler:Moldaver is actually the leader of the last remnants of the New California Republic and is working to activate a cold fusion generator and bring power back to the Wasteland, and Hank is actually a corrupt Vault-Tec executive who destroyed the NCR for petty reasons and all but murdered Lucy's mother in the process]].
* On ''Series/StarTrekEnterprise'', the Xindi plan to destroy Earth because godlike aliens told them that humanity would destroy them in the future. The truth is that the aliens want Earth destroyed so that TheFederation will never form, as this Federation will stop the aliens from conquering the galaxy. Once [[TheCaptain Archer]] learns of this, he sets about convincing the Xindi of the truth, in order to save both races and the entire galaxy.

* In ''Podcast/TheMagnusArchives'', the Magnus Institute seems at first glance to be the "good guys" - for centuries, they've been accumulating knowledge of the occult in order to stop [[EldritchAbomination eldritch gods]] and their followers from ending the world. But then it turns out that they serve their OWN eldritch god, and are only foiling the other gods' apocalypse rituals in order to pave the way for an apocalypse ritual of their own. [[TheBadGuyWins Which they successfully pull off in the season 4 finale, using Jon as the lynchpin]].

* In ''VideoGame/ContraShatteredSoldier'', you discover the Alien invasion that began in the original game, happened because an AncientConspiracy group called the Triumvirate, had a private army invade the Alien planet and steal their technology to make themselves more powerful in ruling the Earth. The Aliens were trying to reclaim what was wrongfully taken from them all along. Bill Rizer's partner Lance Bean finds this out and turns against them.

* ''Franchise/FarCry'': Each of the games features a deconstruction of being the "Good Guy" in a CrapsackWorld; there is no BigGood, there is only you.

* ''Franchise/FireEmblem''

[[folder:Web Original]]
* ''Literature/{{Starwalker}}'' and her crew find out that the person who hired the SpacePirates was the avatar of our sun, who didn't like being used as a doorway 40 years ago (see StableTimeLoop), especially as using the star step drive [[StarKilling shortens the life of stars]]. The crew realise that the star step technology is something [[TheseAreThingsManWasNotMeantToKnow that man is not supposed to know]] (especially as some people would probably look to optimize its destructive potential). [[GreenAesop They decide to rebel against the project, do what they can to heal the stars, and destroy all the copies of information that exist about the project.]]
[[/folder]]

* PlayedForLaughs in ''WesternAnimation/Ducktales2017'', where [[spoiler:the Moonlanders]], who have been tricked into invading under the belief that they're preempting Earth's invasion of their home, overhear their defeated leader declaring he's going to destroy the planet (with all of them still on it) just to deny Scrooge the victory. They have a moment of shock before asking "Wait, are we the bad guys?" While they're raiding the fridge of an innocent family they've BoundAndGagged.
* In the ''WesternAnimation/PhineasAndFerb'' Star Wars special, Candice, Baljeet, and Buford are Stormtroopers. The boys' motives aren't elaborated, but Candice gets a song about how she signed up in the name of law and order. After Phineas saves her life, she begins questioning things and asks Baljeet and Buford, if the Rebellion is so nice, does that mean the Empire might be the bad guys?

** This done again in Season 4. [[spoiler:Adora finds out that the role of She-Ra isn't a heroic one. [[ItSucksToBeTheChosenOne The chosen one]] is meant to be a key to a super weapon used to destroy other planets. The First Ones, whom created She-Ra weren't good, wise and holy people, but intergalactic conquerors, no different than the Horde Empire, if not worse.]]
* ''WesternAnimation/StretchArmstrongAndTheFlexFighters'', where the titular trio learned that their sponsor Jonathan Rook is really the Stretch Monster, and so they've been helping a criminal mastermind throughout the first season. By the time they found this out in its season finale, they ended up becoming fugitives when Rook framed them for the attack on his tower, Rook Unlimited which was started by Rook himself when he tried to dispose of them after they come to realize his plans.

* ''Literature/TheHeroLaughsWhileWalkingThePathOfVengeanceASecondTime'' is all about a FallenHero and his party of the Betrayed using his time-travel fueled second chance to take revenge on a CrapsaccharineWorld which conned him into thinking he was in a stereotypical fantasy game, only to reveal at the very end that his side was composed of genocidal psychopaths who pinned the blame for their mass-murders of innocents on him.

** Per an [[AllThereInTheManual interview]], ultimately {{averted|Trope}} in regard to [[spoiler:the Crimson Flower route]] of ''VideoGame/FireEmblemThreeHouses.'' Part I of the game sets up [[CrystalDragonJesus the Church of Seiros]] -- the major religious institution of the continent of Fodlan and the primary ally of the Officers' Academy, which is the educational institution that [[TheProtagonist Byleth]] is made to teach at for the year -- as well-intentioned yet [[KnightTemplar far-reaching]] and suspicious, and its Archbishop, Rhea, ultimately turns out to [[spoiler:have less-than-savory intentions for Byleth, hoping for [[AssimilationPlot their consciousness to be hijacked by that of her mother (and Fódlan's matron goddess), Sothis]]. While the church is ultimately less than ideal, their status as an all-encompassing evil is something of a RedHerring, and most routes of the game involve Byleth either siding with them directly (Silver Snow, where you reject [[IceQueen Princess Edelgard]]'s plans to [[WeCanRuleTogether bring Fódlan together]] under the [[ResurgentEmpire Adrestian Empire's rule]]) or as a major ally (Azure Moon, where you side with [[DarkAndTroubledPast Prince Dimitri]] of Faerghus, or Verdant Wind, where you side with [[GuileHero Duke Claude]] of the Leicester Alliance); Furthermore, these routes all have the church undergo serious reforms, with the faith being far less encompassing than it was in the past. Siding with Edelgard paints her as a revolutionary and involves having her assimilate the other two countries under her rule and destroying the church entirely, proclaiming both it as well as the [[OurDragonsAreDifferent Children of the Goddess]] -- the draconic race that Sothis, Rhea, Seteth, Flayn, and a few others are a part of -- as being responsible for all of Fódlan's ills since time immemorial. While game does not condemn Byleth for siding with Edelgard, even with the contradictions that her version of history has with the other routes or the misgivings that her allies have, [[AllThereInTheManual the creators of the game]] noted in an interview that the game's worldbuilding is based on Silver Snow by default; In addition to being one of two routes that reveals Rhea's history and Byleth's origins, it is also the default path that the player is put on when they teach Edelgard's class -- one has to [[GuideDangIt go through several hoops]] to actually support Edelgard.]]

** Per an [[AllThereInTheManual interview]], ultimately {{averted|Trope}} in regard to [[spoiler:the Crimson Flower route]] of ''VideoGame/FireEmblemThreeHouses.'' Part I of the game sets up [[CrystalDragonJesus the Church of Seiros]] -- the major religious institution of the continent of Fodlan and the primary ally of the Officers' Academy, which is the educational institution that [[TheProtagonist Byleth]] is made to teach at for the year -- as well-intentioned yet [[KnightTemplar far-reaching]] and suspicious, and its Archbishop, Rhea, ultimately turns out to [[spoiler:have less-than-savory intentions for Byleth, hoping for [[AssimilationPlot their consciousness to be hijacked by that of her mother (and Fódlan's matron goddess), Sothis]]. While the church is ultimately less than ideal, their status as an all-encompassing evil is something of a RedHerring, and most routes of the game involve Byleth either siding with them directly (Silver Snow, where you reject [[IceQueen Princess Edelgard]]'s plans to [[WeCanRuleTogether bring Fódlan together]] under the [[ResurgentEmpire Adrestian Empire's rule]]) or as a major ally (Azure Moon, where you side with [[DarkAndTroubledPast Prince Dimitri]] of Faerghus, or Verdant Wind, where you side with [[GuileHero Duke Claude]] of the Leicester Alliance); Furthermore, these routes all have the church undergo serious reforms, with the faith being far less encompassing than it was in the past. Siding with Edelgard paints her as a revolutionary and involves having her assimilate the other two countries under her rule and destroying the church entirely, proclaiming both it as well as the [[OurDragonsAreDifferent Nabateans]] -- the draconic race that Sothis, Rhea, Seteth, Flayn, and a few others are a part of -- as being responsible for all of Fódlan's ills since time immemorial. While game does not condemn Byleth for siding with Edelgard, even with the contradictions that her version of history has with the other routes or the misgivings that her allies have, [[AllThereInTheManual the creators of the game]] noted in an interview that the game's worldbuilding is based on Silver Snow by default; In addition to being one of two routes that reveals Rhea's history and Byleth's origins, it is also the default path that the player is put on when they teach Edelgard's class -- one has to [[GuideDangIt go through several hoops]] to actually support Edelgard.]]

** Per an [[AllThereInTheManual interview]], ultimately {{averted|Trope}} in regard to [[spoiler:the Crimson Flower route]] of ''VideoGame/FireEmblemThreeHouses.'' Part I of the game sets up [[CrystalDragonJesus the Church of Seiros]] -- the major religious institution of the continent of Fodlan and the primary ally of the Officers' Academy, which is the educational institution that [[TheProtagonist Byleth]] is made to teach at for the year -- as well-intentioned yet [[KnightTemplar far-reaching]] and suspicious, and its Archbishop, Rhea, ultimately turns out to [[spoiler:have less-than-savory intentions for Byleth, hoping for [[AssimilationPlot their consciousness to be hijacked by that of her mother (and Fódlan's matron goddess), Sothis]]. While the church is ultimately less than ideal, their status as an all-encompassing evil is something of a RedHerring, and most routes of the game involve Byleth either siding with them directly (Silver Snow, where you reject [[IceQueen Princess Edelgard]]'s plans to [[VestigalEmpire bring Fódlan under the Adrestian Empire's rule]]) or as a major ally (Azure Moon, where you side with [[DarkAndTroubledPast Prince Dimitri]] of Faerghus, or Verdant Wind, where you side with [[GuileHero Duke Claude]] of the Leicester Alliance); Furthermore, these routes all have the church undergo serious reforms, with the faith being far less encompassing than it was in the past. Siding with Edelgard paints her as a revolutionary and involves having her assimilate the other two countries under her rule and destroying the church entirely, proclaiming both it as well as the [[OurDragonsAreDifferent Nabateans]] -- the draconic race that Sothis, Rhea, Seteth, Flayn, and a few others are a part of -- as being responsible for all of Fódlan's ills since time immemorial. While game does not condemn Byleth for siding with Edelgard, even with the contradictions that her version of history has with the other routes or the misgivings that her allies have, [[AllThereInTheManual the creators of the game]] noted in an interview that the game's worldbuilding is based on Silver Snow by default; In addition to being one of two routes that reveals Rhea's history and Byleth's origins, it is also the default path that the player is put on when they teach Edelgard's class -- one has to [[GuideDangIt go through several hoops]] to actually support Edelgard.]]

* Per an [[AllThereInTheManual interview]], ultimately {{averted|Trope}} in regard to [[spoiler:the Crimson Flower route]] of ''VideoGame/FireEmblemThreeHouses.'' Part I of the game sets up [[CrystalDragonJesus the Church of Seiros]] -- the major religious institution of the continent of Fodlan and the primary ally of the Officers' Academy, which is the educational institution that [[TheProtagonist Byleth]] is made to teach at for the year -- as well-intentioned yet [[KnightTemplar far-reaching]] and suspicious, and its Archbishop, Rhea, ultimately turns out to [[spoiler:have less-than-savory intentions for Byleth, hoping for [[AssimilationPlot their consciousness to be hijacked by that of her mother (and Fódlan's matron goddess), Sothis]]. While the church is ultimately less than ideal, their status as an all-encompassing evil is something of a RedHerring, and most routes of the game involve Byleth either siding with them directly (Silver Snow, where you reject [[IceQueen Princess Edelgard]]'s plans to [[VestigalEmpire bring Fódlan under the Adrestian Empire's rule]]) or as a major ally (Azure Moon, where you side with [[DarkAndTroubledPast Prince Dimitri]] of Faerghus, or Verdant Wind, where you side with [[GuileHero Duke Claude]] of the Leicester Alliance); Furthermore, these routes all have the church undergo serious reforms, with the faith being far less encompassing than it was in the past. Siding with Edelgard paints her as a revolutionary and involves having her assimilate the other two countries under her rule and destroying the church entirely, proclaiming both it as well as the [[OurDragonsAreDifferent Nabateans]] -- the draconic race that Sothis, Rhea, Seteth, Flayn, and a few others are a part of -- as being responsible for all of Fódlan's ills since time immemorial. While game does not condemn Byleth for siding with Edelgard, even with the contradictions that her version of history has with the other routes or the misgivings that her allies have, [[AllThereInTheManual the creators of the game]] noted in an interview that the game's worldbuilding is based on Silver Snow by default; In addition to being one of two routes that reveals Rhea's history and Byleth's origins, it is also the default path that the player is put on when they teach Edelgard's class -- one has to [[GuideDangIt go through several hoops]] to actually support Edelgard.]]

[[folder:Comics]]

[[folder:Live Action TV]]

* PlayedForLaughs in ''WesternAnimation/Ducktales2017,'' where [[spoiler:the Moonlanders]], who have been tricked into invading under the belief that they're preempting Earth's invasion of their home, overhear their defeated leader declaring he's going to destroy the planet (with all of them still on it) just to deny Scrooge the victory. They have a moment of shock before asking "Wait, are we the bad guys?" While they're raiding the fridge of an innocent family they've BoundAndGagged.

* In ''Film/{{Underworld}}'', Selene is a [[OurVampiresAreDifferent vampire]] soldier who has spent several centuries [[FurAgainstFang fighting]] the [[OurWerewolvesAreDifferent Lycans]] in order to [[YouKilledMyFather avenge her family]], and is unfailingly loyal to her maker and ParentalSubstitute, the [[VampireMonarch Vampire Elder Viktor]]. But at the end of the film, she finds out that it was really Viktor who slaughtered her family, and couldn't bring himself to kill her because she reminded him so much of Sonja, his own daughter whom he had put to death for [[FantasticRacism having a]] [[InterspeciesRomance Lycan]] [[MalignedMixedMarriage lover]] and [[HalfHumanHybrid becoming pregnant]] [[HalfBreedDiscrimination with his child]]; her death also instigated the war against the Lycans, who had been [[SlaveRace the vampires' slaves]]. He then [[TheScapegoat blamed the Lycans]] for Selene's family's death, and had her trained to become a Death Dealer so that she could kill the Lycans, who just wanted justice for their inhumane treatment.

* ''LightNovel/TheHeroLaughsWhileWalkingThePathOfVengeanceASecondTime'' is all about a FallenHero and his party of the Betrayed using his time-travel fueled second chance to take revenge on a CrapsaccharineWorld which conned him into thinking he was in a stereotypical fantasy game, only to reveal at the very end that his side was composed of genocidal psychopaths who pinned the blame for their mass-murders of innocents on him.

** ''VideoGame/FarCry2'': Jackal decides that after twenty years of selling low-grade firearms to unstable countries, he's had enough. You, an assassin hired to kill him, end up turning on your former contacts to help him isolate the warring factions (which have now banded together in order to take over Bowa-Sekao as warlords) from 2,000,000 human targets.
** ''VideoGame/FarCry3'': The [[RuthlessModernPirates pirates]] and privateers that control the North and South Rook Islands deal in international human trafficking (slavery) and drugs. You dismantle their operations and kill the bosses so the native tribe can retake their island. Then the tribe's leader tries to force you into killing your friends. If you do as she says, she'll murder you while you're having sex with her so that she can have undisputed worship from both islands, believing she did a favor by killing you in your prime rather than let you wither away from old age, and believing to have your child in her.
** ''VideoGame/FarCry4'': This game is the one that focuses on Wrong Side All Along: Pagan Min, the "King of Kyrat", is a looney Fidel Castro with an iron grip on Kyrat. You join the local rebels to depose him from power. You also eliminate one of the dissenting rebel leaders to keep infighting at a minimum. While you're taking a vacation across the newly freed Kyrat, you discover that the surviving rebel leader has continued the dictatorship, and shifted its priorities to an extreme. Sabal will order religious purges to restore Kyrat's strange and unique religion (and with Pagan's cult of personality permeating the country for decades, along with western influences thanks to the efforts of media rebels such as Rabi Ray Rana Rebel Air, that's pretty much 90% of Kyrat). Amita will attempt to turn Kyrat into one giant drug farm, and conscripts children into her armies to enforce her rule.
** ''VideoGame/FarCry5'': Somewhat disputable, but while it's clear that Joseph Seed's cult isn't doing a good job of "keeping people safe from the apocalypse", what with the various lieutenants screwing up on the keeping people alive thing, the citizens aren't paying attention to the local broadcasts on the global crisis that explains their panic. ''Like Moscow getting nuked''. Also, the Seeds are adamant that the player character is not what they seem, has a greater influence on the world than they realize, and is promptly screwing everyone over by destroying everything the cult tries to build.
* [[PlayingWithATrope Played with]] and, per a [[AllThereInTheManual interview]], ultimately [[AvertedTrope averted]] in regards to [[spoiler:the Crimson Flower route]] of ''VideoGame/FireEmblemThreeHouses.'' Part I of the game sets up [[CrystalDragonJesus the Church of Seiros]] - the major religious institution of the continent of Fodlan and the primary ally of the Officers' Academy, which is the educational institution that [[TheProtagonist Byleth]] is made to teach at for the year - as well-intentioned yet [[KnightTemplar far-reaching]] and suspicious, and its Archbishop, Rhea, ultimately turns out to [[spoiler:have less-than-savory intentions for Byleth, hoping that their [[AssimilationPlot consciousness is hijacked by that of her mother (and Fódlan's matron goddess), Sothis.]] While the church is ultimately less than ideal, their status as an all-encompassing evil is something of a RedHerring, and most routes of the game involve Byleth either siding with them directly (Silver Snow, where you reject [[IceQueen Princess Edelgard's]] plans to [[VestigalEmpire bring Fódlan under the Adrestian Empire's rule]]) or as a major ally (Azure Moon, where you side with [[DarkAndTroubledPast Prince Dimitri]] of Faerghus, or Verdant Wind, where you side with [[GuileHero Duke Claude]] of the Leicester Alliance); Furthermore, these routes all have the church undergo serious reforms, with the faith being far less encompassing than it was in the past. Siding with Edelgard paints her as a revolutionary and involves having her assimilate the other two countries under her rule and destroying the church entirely, proclaiming both it as well as the [[OurDragonsAreDifferent Nabateans]] - the draconic race that Sothis, Rhea, Seteth, Flayn, and a few others are a part of - as being responsible for all of Fódlan's ills since time immemorial. While game does not condemn Byleth for siding with Edelgard, even with the contradictions that her version of history has with the other routes or the misgivings that her allies have, [[AllThereInTheManual the creators of the game]] noted in an interview that the game's worldbuilding is based on Silver Snow by default; In addition to being one of two routes that reveals Rhea's history and Byleth's origins, it is also the default path that the player is put on when they teach Edelgard's class - one has to [[GuideDangIt go through several hoops]] to actually support Edelgard.]]

* In ''VideoGame/GuildWars Prophecies'', when the heroes arrive in Kryta, they find the ruling White Mantle fighting rebels, the Shining Blade. They initally join with the Mantle, but when the Shining Blade point them to the truth about the Mantle – they're rounding up people identified as a threat to their "gods" to ritualistically execute them – they switch sides.
* In ''VideoGame/JadeEmpire'', you find out that your mentor has been playing you all along, and basically used you as a tool to take over the empire. Not that the Emperor was much better.
* This gets ZigZagged in ''VideoGame/NieR''. Early on in the game, the main character's daughter/sister gets abducted by the mysterious Shadowlord, who's ostensibly the leader of malevolent monsters or Shades that have been terrorizing the people. You therefore embark on a quest to get her back, cutting down anyone who stands in your way. [[spoiler:However, it's eventually revealed that the Shades are the ''original'' humans who separated themselves from their bodies in as a last-ditch effort to save themselves from extinction, and a lot of the Shades you killed weren't malevolent at all. The characters you've been following were Replicants that were meant to be vessels that the Shades could inhabit when the time was right. The ''real'' villains of the story turn out to be a pair of {{Well Intentioned Extremist}}s who were manipulating everyone to ensure that all the Shades would get assimilated, at the cost of the Replicants essentially being [[GrandTheftMe overwritten]]. And the Shadowlord is both the main character's original incarnation, and the only one who can prevent all the Shades from degenerating into mindless beasts. Since the game ends with you successfully killing the Shadowlord, you've inadvertently doomed humanity to extinction in order to save the ones you love.]]

[[folder:Web Comics]]
* Happened to Schlock's mother in ''WebComic/SchlockMercenary''. Schlock's human grandmother was a slave trader and she duped her [[InterspeciesRomance amorph daughter]] into fighting the hero (Schlock's father) who was trying to stop her. Due to the unique nature of amorph biology the fight ended up with the personalities of both Schlock's parents being destroyed and their bodies merging to produce Schlock.

* In the third ''Anime/RebuildOfEvangelion'' movie, poor Shinji falls victim to two instances of this: Just after having left the RenegadeSplinterFaction of the organization he used to work for, he finds out that said organization, ''including his own father Gendo'', has been plotting doomsday for quite a while, and, in fact, sucessfully [[NiceJobBreakingItHero set him up to cause it]] ''for them'' in a futile attempt to save his LoveInterest, and, in fact, brought the two of them together for that exact purpose. Then, he gets told that he can fix the now nigh-inhabitable planet by obtaining a certain ArtifactOfDoom, which he sets out to get, having to [[WeUsedToBeFriends fight his former roommate and friend Asuka]] in the process. When he actually gets his hands on the artifacts, they do, [[UnwittingPawn obviously]], cause yet another near-apocalypse as Shinji [[MyGodWhatHaveIDone stares in horror]].
* ''Manga/PhantomThiefJeanne'', Finn Fish is the right-hand woman of Lucifer who has been using Jeanne, and the rival angel is trying to stop Finn as he knows that she has been possessed by evil.

* ''Film/StreetKings'': Detective Ludlow and his team are supported by Captain Wander in their CowboyCop tendencies. A former partner of Ludlow then starts snitching to the antagonistic Captain Biggs from InternalAffairs before being killed in an apparently random shooting. Ludlow eventually discovers that Biggs's investigation was entirely justified and Wander has been running a wholesale extortion and murder racket behind Ludlow's back.
* In ''Film/CaptainMarvel2019'', it turns out [[spoiler:Carol Danvers and Nick Fury are unwittingly helping the genocidal and imperialistic Kree exterminate the Skrulls who, while themselves ruthless, were only trying to survive and find a new home for themselves. Carol in particular is ''pissed'' that she was being played like a cheap kazoo for the past six years, and pulls a HeelFaceTurn to stop them.]]

* On ''Series/StarTrekEnterprise'', the Xindi plan to destroy Earth because godlike aliens told them that humanity would destroy them in the future. The truth is that the aliens want Earth destroyed so that TheFederation will never form, as this Federation will stop the aliens from conquering the galaxy. Once [[TheCaptain Archer]] learns of this, he sets about convincing the Xindi of the truth, in order to save both races and the entire galaxy.

* In ''Podcast/TheMagnusArchives'', the Magnus Institute seems at first glance to be the "good guys" - for centuries, they've been accumulating knowledge of the occult in order to stop [[EldritchAbomination eldritch gods]] and their followers from ending the world. But then it turns out that they serve their OWN eldritch god, and are only foiling the other gods' apocalypse rituals in order to pave the way for an apocalypse ritual of their own. [[TheBadGuyWins Which they successfully pull off in the season 4 finale, using Jon as the lynchpin.]]

* In ''VideoGame/SpecOpsTheLine'', Captain Walker and his team are frequently the ''sole'' reason things get worse in Dubai. They destroy the water supply, massacre civilians, and commit other atrocities in the name of fighting evil. [[HeelRealization Whoops.]]

* In ''VideoGame/JadeEmpire'', you find out that your mentor has been playing you all along, and basically used you as a tool to take over the empire. Not that the Emperor was much better.
* Altair spends most of ''VideoGame/AssassinsCreedI'' killing key Templar figures on both sides of the Crusades. In the end, he is told that his master is a former Templar himself who was merely trying to eliminate the competition. While this doesn't turn him against the Assassins, he ends up fighting and killing his mentor.
* In ''VideoGame/RatchetAndClankGoingCommando'', the titular duo are hired by [=MegaCorp=] to track down a mysterious thief and recover a stolen experiment. After defeating the thief in a ClimaxBoss fight halfway through the game, they learn that the thief is a former [=MegaCorp=] geneticist who stole the experiment, the [[KillerRabbit Protopet]], before it could be unleashed on the galaxy with devastating consequences. The game even manages to keep the same enemy mooks after switching antagonists, as Thugs 4 Less are quickly enticed with a better offer to change employers. [[spoiler: It later turns out that not even [=MegaCorp=] are the real antagonists: the whole thing was an EngineeredHeroics plot by [[FakeUltimateHero Captain Qwark]], and the heroes now have to save the galaxy from his stupidity.]]

* In ''VideoGame/BravelyDefault'', [[TheEmpire Eternia]] and its Jobmasters, under the leadership of the supposed BigBad Braev Lee, have been trying to usher in an era where people are not dependent on the elemental Crystals. The party opposes them, told by ExpositionFairy Airy that by awakening the Crystals, they would summon the Holy Pillar to cleanse evil from the world. As it turns out, Airy [[TreacherousAdvisor is in fact]] the true BigBad and by awakening the Crystals, the party is further destabilizing all the different Luxendarcs while allowing Airy's father, [[GreaterScopeVillain Ouroboros]], to devour their world. [[MultipleEndings Either]] they [[ExplosiveOverclocking over-awaken]] a Crystal to destroy it and set back the villain's plans by several centuries, or they resolve to persist, hoping that in the end they could face off against and destroy Ouroboros.
* This gets ZigZagged in ''VideoGame/NieR''. Early on in the game, the main character's daughter/sister gets abducted by the mysterious Shadowlord, who's ostensibly the leader of malevolent monsters or Shades that have been terrorizing the people. You therefore embark on a quest to get her back, cutting down anyone who stands in your way. [[spoiler:However, it's eventually revealed that the Shades are the ''original'' humans who separated themselves from their bodies in as a last-ditch effort to save themselves from extinction, and a lot of the Shades you killed weren't malevolent at all. The characters you've been following were Replicants that were meant to be vessels that the Shades could inhabit when the time was right. The ''real'' villains of the story turn out to be a pair of {{Well Intentioned Extremist}}s who were manipulating everyone to ensure that all the Shades would get assimilated, at the cost of the Replicants essentially being [[GrandTheftMe overwritten]]. And the Shadowlord is both the main character's original incarnation, and the only one who can prevent all the Shades from degenerating into mindless beasts. Since the game ends with you successfully killing the Shadowlord, you've inadvertently doomed humanity to extinction in order to save the ones you love.]]
* In ''VideoGame/PokemonMysteryDungeonExplorers'', the protagonists join the explorer from the future Dusknoir to stop Grovyle from stealing the Time Gears, with will [[BadFuture freeze the planet in time]], which Dusknoir went back in time to prevent. Turns out that Grovyle is the one trying to SetRightWhatOnceWentWrong, because even though there's temporary paralysis of the area where the Time Gear was taken, they need to be placed in Temporal Tower to stop Dialga from [[MadGod going Primal]] and avoid the BadFuture, and Dusknoir is working for Primal Dialga all along.

* The opening plot of ''WesternAnimation/SheRaAndThePrincessesOfPower'', has young protagonist, Adora, finding out she was raised and trained to fight and serve the oppressive, conquering Horde Empire, and her mentor Shadow Weaver was using and grooming her all along. After she discovers she is the next chosen one to become She-Ra, she joins the rebellion against them.
** This done again in Season 4. [[spoiler: Adora finds out that the role of She-Ra isn't a heroic one. [[ItSucksToBeTheChosenOne The chosen one]] is meant to be a key to a super weapon used to destroy other planets. The First Ones, whom created She-Ra weren't good, wise and holy people, but intergalactic conquerors, no different than the Horde Empire, if not worse.]]
* PlayedForLaughs in ''WesternAnimation/Ducktales2017,'' where [[spoiler: the Moonlanders]], who have been tricked into invading under the belief that they're preempting Earth's invasion of their home, overhear their defeated leader declaring he's going to destroy the planet (with all of them still on it) just to deny Scrooge the victory. They have a moment of shock before asking "Wait, are we the bad guys?" While they're raiding the fridge of an innocent family they've BoundAndGagged.

--> '''Candice:''' Besides, didn't we just blow up a planet?
--> '''Baljeet:''' That ''is'' sort of hard to justify, ethically.

* In ''VideoGame/BravelyDefault'', [[TheEmpire Eternia]] and its Jobmasters, under the leadership of the supposed BigBad Braev Lee, have been trying to usher in an era where people are not dependent on the elemental Crystals. The party opposes them, told by ExpositionFairy Airy that by awakening the Crystals, they would summon the Holy Pillar to cleanse evil from the world. As it turns out, Airy [[TreacherousAdvisor is in fact]] the true BigBad and by awakening the Crystals, the party is further destabilizing all the different Luxendarcs. [[MultipleEndings Either]] they [[ExplosiveOverclocking over-awaken]] a Crystal to destroy it and set back the villain's plans by several centuries, or they resolve to persist, hoping that in the end they could face off against and destroy the GreaterScopeVillain, Ouroboros.

[[folder: Western Animation]]

* In ''VideoGame/TalesOfPhantasia'', the villain is basically trying to save his people, and create a mana seed. In fact, he helps restore mana, since humans and half-elves have been using it up. Cless, Chester, and the rest are not exactly villains, but they are on the wrong side, as a result of only understanding the problem from a human point of view.
** It doesn't help that the villain never explained his intentions. Instead of trying to reason with humanity, explaining that their actions were harming the Mana Tree (which would also cause problems for them), he went straight to declaring war and trying to destroy everything in his way. The protagonists, and thus, the players, only discover his goals at the very end - even ''then'', it was a different character doing the exposition.
** They also weren't really on the "wrong side" so to speak. Dhaos really was a threat to them and humanity and there wasn't the possibility of negotiation at that point. The situation just wasn't quite as black and white as it appeared.

* ''LightNovel/NidomeNoYuusha'' is all about a FallenHero and his party of the Betrayed using his time-travel fueled second chance to take revenge on a CrapsaccharineWorld which conned him into thinking he was in a stereotypical fantasy game, only to reveal at the very end that his side was composed of genocidal psychopaths who pinned the blame for their mass-murders of innocents on him.

Subtrope of EvilRunningGood; this is specific in that the antagonist is (also) a good guy (while that trope can have actual bad guys as antagonists). Compare UnwittingPawn.

* [[PlayingWithATrope Played with]] and, per a [[AllThereInTheManual interview]], ultimately [[AvertedTrope averted]] in regards to [[spoiler:the Crimson Flower route]] of ''VideoGame/FireEmblemThreeHouses.'' Part I of the game sets up [[CrystalDragonJesus the Church of Seiros]] - the major religious institution of the continent of Fodlan and the primary ally of the Officers' Academy, which is the educational institution that [[TheProtagonist Byleth]] is made to teach at for the year - as well-intentioned yet [[KnightTemplar far-reaching]] and suspicious, and its Archbishop, Rhea, ultimately turns out to [[spoiler:have less-than-savory intentions for Byleth, hoping that their [[AssimilationPlot consciousness is hijacked with that of her mother (and Fodlan's matron goddess), Sothis.]] While the church is ultimately less than ideal, their status as an all-encompassing evil is something of a RedHerring, and most routes of the game involve Byleth either siding with them directly (Silver Snow, where you reject [[IceQueen Princess Edelgard's]] plans to [[VestigalEmpire bring Fodlan under the Adrestian Empire's rule]]) or as a major ally (Azure Moon, where you side with [[DarkAndTroubledPast Prince Dimitri]] of Faerghus, or Verdant Wind, where you side with [[TheSchemer Duke Claude]] of the Leicester Alliance); Furthermore, these routes all have the church go under serious reforms, with the faith being far less encompassing than it was in the past. Siding with Edelgard paints her as a revolutionary and involves having her assimilate the other two countries under her rule and destroying the church entirely, proclaiming both it as well as the [[OurDragonsAreDifferent Nabateans]] - the draconic race that Sothis, Rhea, Seteth, Flayn, and a few others are a part of - as being responsible for all of Fodlan's ills since time immemorial. While game does not condemn Byleth for siding with Edelgard, even with the contradictions that her version of history has with the other routes or the misgivings that her allies have, [[AllThereInTheManual the creators of the game]] noted in an interview that the game's worldbuilding is based on Silver Snow by default; In addition to being one of two routes that reveals Rhea's history and Byleth's origins, it is also the default path that the player is put on when they teach Edelgard's class - one has to [[GuideDangIt go through several hoops]] to actually support Edelgard.]]

* In ''VideoGame/BravelyDefault'', [[TheEmpire Eternia]] and its Jobmasters, under the leadership of the supposed BigBad Brav Lee, have been trying to usher in an era where people are not dependent on the elemental Crystals. The party opposes them, told by ExpositionFairy Airy that by Awakening the Crystals, they would summon the Holy Pillar to cleanse evil from the world. As it turns out, Airy [[TreacherousAdvisor is in fact]] the true BigBad and by Awakening the Crystals, the party is further destabilizing all the different Luxendarcs. [[MultipleEndings Either]] they [[ExplosiveOverclocking Over-Awaken]] a Crystal to destroy it and set back the villain's plans by several centuries, or they resolve to persist, hoping that in the end they could face off against and destroy the GreaterScopeVillain, Ouroboros.
* This gets ZigZagged in ''{{VideoGame/Nier}}''. Early on in the game, the main character's daughter/sister gets abducted by the mysterious Shadowlord, who's ostensibly the leader of malevolent monsters or Shades that have been terrorizing the people. You therefore embark on a quest to get her back, cutting down anyone who stands in your way. [[spoiler:However, it's eventually revealed that the Shades are the ''original'' humans who separated themselves from their bodies in as a last-ditch effort to save themselves from extinction, and a lot of the Shades you killed weren't malevolent at all. The characters you've been following were Replicants that were meant to be vessels that the Shades could inhabit when the time was right. The ''real'' villains of the story turn out to be a pair of {{WellIntentionedExtremist}}s who were manipulating everyone to ensure that all the Shades would get assimilated, at the cost of the Replicants essentially being [[GrandTheftMe overwritten]]. And the Shadowlord is both the main character's original incarnation, and the only one who can prevent all the Shades from degenerating into mindless beasts. Since the game ends with you successfully killing the Shadowlord, you've inadvertently doomed humanity to extinction in order to save the ones you love.]]

-->--'''Never Existed''', ''Music/{{Keldian}}''

* ''VideoGame/FarCry'': Each of the games features a deconstruction of being the "Good Guy" in a CrapsackWorld; there is no BigGood, there is only you.