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- Naruto has an interesting example of this. Itachi is by no means fooled into thinking he's working for the greater good or threatened into fighting for the big bads. He just wants to keep his baby brother safe and the best place to do that would be by infiltrating the Akatsuki and watching Konoha. He also prevented another ninja war by putting down the Uchiha rebellion, but by the time of the series he's almost certainly realized how much of that was Danzo manipulating him. It's very likely, though not explicit, that he was informed that if he preserved secrecy by following the script, he'd be allowed to leave Sasuke alive, but if he forced them to assign it to some other Anbu, they'd kill him, too.
- Magic Knight Rayearth's first Big Bad Zagato, who has kidnapped the princess and is destroying the world? Turns out the princess kidnapped herself so she could try to stop loving Zagato, and the destruction that's going on is the result of her inner turmoil. This is more of a case of "not wholly evil" than "good," however.. He may have been motivated by love and disgust for the corrupt system his world ran on, but he still did some things that are hard to describe as anything but evil, including trying to kill the Magic Knights (who are the only true innocents in the entire story and likely would have at least been sympathetic if he even tried to explain things), manipulating and lying to Ascot so he would be a loyal minion, allowing Alcyone to die from her battle wounds for her failures in the manga, etc.
- Dr. Franken von Vogler in Giant Robo. Made out to be a mad scientist responsible for a giant catastrophe 10 years ago by ignoring all risks and his fellow scientists in the experiment with the Shizuma Drive, it eventually turns out that he was the only one who opposed the project and the seemingly "good professor" was among the people who wanted to go through with it. All 5 of the inventors survived, but Vogler was believed to be dead, so the remaining 4 decided to cover the whole incident in lies and put all the blame on Vogler. Really no wonder why the Big Bad wants revenge.
- Laxus Dreyar in Fairy Tail. His attempt to take over the guild is nothing more than a teenage temper tantrum fueled by fear that he wasn't getting the proper credit for his accomplishments, always being compared to his grandfather (who is also the guildmaster). He tries to kill everyone in Magnolia Town with Fairy Law, a spell designed to target those the caster sees as enemies, and it doesn't hit a single person.
- Puella Magi Madoka Magica has an exceptionally sad example with Homura Akemi. It turns out she's a time traveler who knows all about Kyubey's ulterior motives for empowering teenage girls, and her sole reason for living is to try to keep Madoka safe. Unfortunately, circumstances conspire to make this a seemingly impossible task, no matter how many times Homura goes back to try to fix things. Her stoic (and at times, callous) demeanor hides the fact that she's rapidly approaching her Despair Event Horizon after watching her best friend die (or worse) dozens of times.
- In Bleach, Ichigo's Superpowered Evil Side turned out to not be evil at all, merely overprotective. It turns out the "Inner Hollow" was Ichigo's true Zanpakuto spirit all along, one that was formed with the remnants of a Hollow as its base. "Inner Hollow" only ever wanted to make Ichigo stronger and keep him safe.
- "Good" might be a stretch, but it turns out that Gin Ichimaru was plotting to take down Sousuke Aizen since his own childhood, becoming Aizen's right-hand man just to ensure he'd be in position when the time came to strike.
- Kill la Kill gives us Satsuki Kiryuin, who was introduced as a dictator who antagonized Ryuko at every turn. Everything she did was just to make Ryuko stronger and more prepared for what was to come. And to shape all of the Honnouji Academy students into a Badass Army that could take down the real villains.
- Kenichi: The Mightiest Disciple: Saiga Furinji, previously touted as a major antagonist in the story, is revealed near the end of the manga to have been this, or at least Yami's greatest Token Good Teammate, especially considering the revelation that his wife's/Miu's mother's murder, which he'd previously been thought to be responsible for, was in fact carried out by an Evil Former Friend disguised as him.
- In The Circumstances Leading To Waltraute's Marriage, it turns out Loki's shady activities were his attempts to prevent Ragnarok, not start it.
- The Shitennou in Sailor Moon Crystal. All of them were Brainwashed and Crazy, but they were freed from it by the Sailor Soldiers. Unfortunately, they had a nasty price to pay for it, as they soon learn courtesy of an energy wave.
- The Book of Darkness from Magical Girl Lyrical Nanoha A's was not only good all along but was actually the biggest victim in the entire season, possibly the entire franchise. All the problems they end up causing were because of bad programming rather than malice.
- I Kill Giants has the Titan. Initially believed to be the most powerful and most evil of giants, it turns out that the Titan is a being of near pure benevolence that only wants to help the main character deal with the trauma of her mother's impending death.
- Clash of the Elements: Gemini discusses this trope with Mallow in Part 2, more specifically referring to Domino when he does so.
- Avalon: The Angels ending up not having had the destruction of mankind as their goal, nor would accomplishing their goal have that as a biproduct. Jay, Kay and Shin also are revealed that be this, as their actions against NERV caused the needless war to come to an end sooner, with less lose of life and property in an attempt to prevent their Bad Future.
- Calvin and Hobbes: The Series has a rather ambiguous example: the final story has two distinct plots, one involving Slender Man and the other concerning the return of Thunderstorm and Shadow. The climax involves the Slender Man causing the latter two to disappear (it's never stated as to whether they were killed, but the final line of that chapter shows him waving to the heroes as they leave, his mission complete.
- Dean of the X-Trio in Pokeumans revealed himself to be one of Mew's agents, having worked his way into the heart of the Pokextintion organisation. It's a shame he had to do all sorts of terrible things to get there though.
- Maylus Revenge: Empress Roll.
- In Warhammer 40,000: Rise Of The Tau, the Orks turn out to be this. Gork and Mork (who are both Old Ones) were forced to turn them into insane savages to ensure their survival after the War in Heaven. They end up becoming valuable allies for the Imperium against the Tau. Also, Magnus the Red, who kept a part of himself untouched by Chaos so when the Emperor ascended, he was able to purify Magnus of the corruption and allow him to reunite the Primarchs for the final battle against the Tau and the C'tan.
- In Hocus Pocus, Winifred raises her former lover Billy (who she had murdered long ago) from the dead as a zombie, and orders him to chase the protagonists. Billy spends most of the film doing so, unable to talk because his mouth is sewn shut. When he finally cuts the stitches holding his mouth shut and manages to speak, he curses Winifred and starts helping the heroes, which was apparently what he intended to do from the start.
- In D3: The Mighty Ducks new coach Ted Orion rejects the Ducks' view of having fun, changes them from the Ducks to the freshman Warriors, strips Charlie Conway of his rank as team captain, and even goes as far as saying "The Ducks are dead!" The truth is he was trying to teach them "two-way hockey," master the art of defense, and mature their hockey playing. Then, he would give back their Duck jerseys. Charlie, combined with adolescence pains and resentment for Bombay "abandoning" them, misunderstood greatly and alienated himself from his friends. Then, Bombay revealed that Orion was on their side all along and that he told Orion how great Charlie really was. Orion proved all this when he accepted Charlie's return, and refused to let the Eden Hall Academy board withdraw their scholarships for poor performance, threatening to resign if they are expelled. Good thing Bombay was there to help. And not only did Orion return the team the Duck jerseys, but he also reinstated Charlie as team captain in the J.V.-Varsity Showdown.
- The twist of The Rock is that Hummel never intended to actually launch the gas into San Francisco and it was all a big bluff to force the Pentagon to pay money for the families of dead Marines. Sadly, Hummel realizes too late that many of his underlings were in this for the money and it causes a mutiny.
- In The Hateful 8 former southern marauder Chris Mannix tries to convince his fellow lodgers he's the new sheriff in a local town, but is unable to prove it. As it turns out, he's one of the few characters on the side of the law, and one of the few completely honest about their past.
- In the Eternal Champion series, Ekrose (an incarnation of Elric) goes to war against the Eldren. He finds this trope applies to them, is torn by his loyalties but in the end kills the entire human race when they won't retreat.
- Aleister Crowley in R.A. Wilson's The Masks of Illuminati. He is made out to be the Big Bad of the novel, but all his crimes happen off-screen, and it turns out they didn't happen at all; either him in disguise, or his lackeys simply lied to the protagonist about them. His aim is to illuminate the protagonist by blowing his mind, as well as a benevolent equivalent of For the Evulz-thinking.
- Harry Potter series:
- Sirius Black for the majority of the third book is thought to be Voldemort's most loyal servant, the one who betrayed Harry's parents and ready to avenge his master. It turns out that in fact, he's completely innocent, the one who betrayed James and Lily is their other friend Peter Pettigrew aka Scabbers.
- Severus Snape. Turns out everything he did in the books, he did while working for Dumbledore and following his orders, which includes killing Dumbledore, and all in the name of his unrequited love for Harry's mother, Lily, and the guilt he feels over his role in her death.
- When she is introduced in the ninth Haruhi Suzumiya novel, Sasaki is set up to appear as the title character's Evil Counterpart. However, it turns out that she really had no idea what was actually going on, and had no idea that her new friends were the real villains, and when the Masquerade gets broken for her, Sasaki secretly allies with Kyon to oppose those who wish to cause Haruhi harm.
- Jeremiah Paulson from the Dale Brown book A Time for Patriots seemed to be the leader of a Right-Wing Militia Fanatic group. Eventually, it turns out that he wasn't responsible.
- Mab is one of the most terrifying entities in the Fantasy Kitchen Sink world of The Dresden Files, never failing to freak Harry out whenever she appears. Sometime around the seventh book, the heros start to suspect she may have gone off the deep end. They are, understandably, very nervous about this, as she's a Nigh Invulnerable Physical God who the author confirms could Curb Stomp the entire White Council. Come Cold Days, however, and it's revealed that she protects our entire reality from being destroyed by Outsiders. She's still an extremely scary being, however.
- Thrawn and his Empire from the The Thrawn Trilogy were the antagonists that the heroes had to deal with in the first EU novels. The book Outbound Flight reveals that Thrawn was uniting the galaxy through an Imperial conquest to build up a strong enough galaxy in order to repel the extragalactic invading aliens known as the Vong.
- Abe Mazur from Vampire Academy has the reputation of a gangster and is good at intimidating people. But his role in the series is not that of a mean mob boss. Just a concerned father to Rose. He is looking out for her best interests.
- In the episode "Folsom Prison Blues" (S02, Ep19) of Supernatural, the warden of the prison turns out to be John Winchester's friend and helps Sam and Dean escape.
- Played for laughs in the first episode of Sherlock. John is summoned (read: almost kidnapped) by an ominous, well-connected man who offers him money for updates on Sherlock's movements. "I worry about him constantly...we have what you might call a "difficult relationship." John assumes he's a criminal mastermind, and the viewer could be forgiven for thinking he's Moriarty. It turns out he's just Sherlock's equally-strange older brother.
- Takatora Kureshima/Kamen Rider Zangetsu in Kamen Rider Gaim initially seems to be the Big Bad, particularly how he tries to play Hope Crusher for Kouta. However, it's gradually revealed that Takatora has been lied to by his inner circle and thinks that only 1/7th of the world's population, at best, can be saved from the Forest of Helheim's invasion, which he views as unfortunate but better than the alternative. When Kouta reveals that there's an intelligent species with control over Helheim's flora (yet another thing his inner circle hid from him), Takatora gladly joins forces with him in the hopes that they can convince these Overlords to call off the invasion; sadly, at this point the inner circle (plus Takatora's own brother) decides he's outlived his usefulness...
- In The Outer Limits (1995) episode "Something About Harry", a teenager suspects that his mom's new tenant is an alien infiltrator when people start disappearing around town, whom the tenant is melting into green goo with a futuristic gun. The tenant was actually a U.S. government agent, and everyone he killed was one of the real aliens. The teenager's mother is the one who had really been replaced by the alien parasites.
- In the Agents Of SHIELD episode "A Hen in the Wolfhouse", Simmons's cover at HYDRA is under threat from their security team, led by Bobbi Morse. When her cover is completely blown, Morse takes out the rest of the security team and tells Simmons that Coulson has arranged their extraction.
- After getting close — very close — to Rosalind Price, the head of the newly formed Advanced Threat Containment Unit, which has been capturing Inhumans and keeping them in storage until a "cure" can be found, Coulson reveals to her that he already knows that her organization is overseen by HYDRA. He is correct — but Rosalind herself was completely unaware and, once she convinces Coulson of her innocence, is willing to work with him to bring it down.
- Marchlands spends four episodes playing on classic expectations of a poltergeist, but the final episode reveals that the ghost never actually tries to harm anyone—she is only trying to expose the mysterious circumstances of her death, and on one occasion she even saves an epileptic boy from drowning in a bathtub. This is made even clearer at the end, when even the resident Agent Scully, Amy's mother, admits, "I think Alice was really a good girl all along."
- Wet Hot American Summer: First Day Of Camp: The Falcon, President Reagan's personal assassin, was apparently this. As soon as it's revealed, however, Beth points out that it makes no sense at all, since The Falcon had repeatedly tried to kill her and had successfully killed two of her friends along with several others. The Falcon says that he'd like to explain but there's somewhere he really has to be.
- A character on Supergirl is traditionally a villain in the comics, but is revealed to be this on the television show. This is because the character, Hank Henshaw, is actually a disguised J'onn J'onzz, the Martian Manhunter, who is a hero in the comics.
- In Super Smash Bros. Brawl's Subspace Emissary mode, King Dedede spends most of the story trying to take fighters that have been turned into trophies. Then after everybody except the three that he did manage to get face down Tabuu and get trophified, the badges he placed on those three turn them back to normal.
- Of course, the fact that a major cutscene revealing why he did this (in which he's present while Meta Knight's ship gets stolen) got removed in the final cut does complicate this. With that said, Dedede acting like a dick for no reason would still be quite in character for him.
- In the Kirby series of video games, King Dedede's almost always portrayed as the Big Bad in the beginning of a given game, but usually turns out to be either this or just an innocent jerk. The most blatant case is probably Kirby's Adventure/Nightmare in Dream Land, where he destroys the Star Rod and prevents everyone in Dream Land from dreaming. It turns out he was just trying to stop Nightmare from taking over the Fountain of Dreams.
- Landia in Kirbys Return To Dreamland. Though Magolor claims that it's threatening Halcandra, in reality, it's the planet's guardian and lives to prevent its treasures from falling into the wrong hands; the Lor Starcutter and Master Crown being two of them. After Kirby and friends beat it up as a result of the misinformation, it immediately aids them in stopping Magolor once his true intentions come to light.
- Angela Cross, the true identity of the Masked Thief in Ratchet & Clank: Going Commando. Angela has been working against Megacorp to prevent the release of the Protopet, as it is a violent carnivorous creature that also repeatedly reproduces offspring at the drop of a hat, and if it got out could very well threaten everything in the galaxy.
- Depending on what ending the player gets, Anne of Silent Hill: Downpour was in the right all along. In all but the best ending, Murphy killed her father as part of a prison deal, and in the worst ending, he also killed his own son, making his reasons for revenge entirely moot.
- Cynder, the Big Bad of the first game in The Legend of Spyro trilogy turned out to be Brainwashed and Crazy. After Spyro defeated her, she returned to her normal self and eventually fell in love with Spyro.
- The Boss from Metal Gear Solid 3: Snake Eater. Even before The Reveal that she's a Fake Defector, it's made quite clear that she's a good woman.
- And in Metal Gear Solid 4: Guns of the Patriots, Revolver Ocelot is revealed to have been noble in his goals from the very start, working to destroy the Patriots for good and also working save Big Boss, who he admired deeply. All while being seen as a terrorist the whole time.
- Grovyle in Pokémon Mystery Dungeon: Explorers is initially presented as a villain who's trying to throw off the world's balance by swiping the Time Gears. However, it turns out that he's actually trying to save the world, as any ill effects caused by the removal of the gears are temporary, and they're needed to stop what's really going to doom the world. If only he had bothered trying to explain this before you get captured by the real villain along with him...
- Pokémon Mystery Dungeon: Gates to Infinity has Hydreigon, who looks pure evil, is seen attacking Munna in the opening, and is later stated to be the cause of the world's impending destruction. However, everything but his appearance turns out to be a lie, and he's actually the one who called the player into the Pokemon world to act as its savior. He proves to be one of the kindest and most heroic characters in the series and a shining example of Dark Is Not Evil.
- In Super Robot Wars UX Arnie and Saya get to have a conversation with Jin and Ayul where Arnie fully realizes that Jin truly has no ill intent. Jin just really, really wants to stop the apocalypse from coming about and will do anything to defeat you to make that happen.
- Applies to an entire species: the Geth, as of Mass Effect 2. Turns out the ones you've been fighting are a sort of rebel faction who worship the Reapers. Normal Geth refer to these as "Heretic" Geth, you learn this after meeting one. More a case of True Neutral All Along: Most of their species have no beef with anyone else in the galaxy and just want to be left alone.
- Tears to Tiara 2 has the Recurring Boss Izebel. Played up as traitor and Deceptive Disciple she has in fact the entire time been subtly helping La Résistance behind the scenes. Her fight with Hamil were to both train him and test his abilities to make sure he's good enough to take on The Empire. And the entire thing, including her "betrayal" was ordered by the superior whom she supposedly betrayed before he took his own life.
- Five Nights at Freddy's 2: As it turns out, the animatronics fall into this trope. During the mini games, you can see that Freddy attempts to rescue some kids from the real murderer, but fails. As for the other animatronics, they just seem like they want to entertain the children.
- Five Nights at Freddy's 3 reveals that the classic animatronics—Freddy, Chica, Bonnie, and Foxy—as well as the Puppet were Good. They were trying to find and stop the homicidal Purple Man. Because their spirits were that of children, they couldn't identify him properly or tell him apart from other adults. They were using the only context clue they had: a security guard's uniform. Turns out that the Puppet is the Big Good! He's the one who revived the five murdered children as the suits so they could find their killer, even though he is heavily implied to be a dead child himself.
- Lunar: Eternal Blue: Despite apparently working for the Big Bad Ghaleon eventually reveals himself to be this. This is especially surprising because Ghaleon was the Big Bad of the first game; everything that he does in the second game is a secret effort to atone for his previous actions.
- The primary antagonist of Mega Man IV is Dr. Cossack, a Russian scientist who sent eight of his robots to attack Mega Man to prove his genius. Except that he was being blackmailed by Dr. Wily into doing his work for him, and never had evil ambitions of his own. In the following game, where Dr. Light is kidnapped, Cossack serves as an ally in his place.
- The villains of Golden Sun, Saturos and Menardi, turn out to not only be fighting to save the world, but have only resorted to brute force because not only did the elders of Vale refuse to listen to their warnings about the imminent apocalypse, but their hometown is the first place on the apocalypse's chopping block. They're still grade-A Jerk Asses who get their fair share of Kick the Dog moments, but at least their hearts are in the right place. Alex, not so much by a long shot.
- In Until Dawn, the Flamethrower Guy is initially assumed to be the Serial Killer hunting the teens, but is eventually revealed to be separate entity that only wanted to protect the kids from the wendigos. In addition, the Serial Killer is just one of the kids trying to teach the others a lesson and was completely unaware anyone was in any danger, and Dr. Hill is said kid's conscience.
- In Shin Megami Tensei, the two major powers are YHVH, an insane Tautological Templar, and Lucifer, a Well-Intentioned Extremist with Jerkass tendencies. Lucifer is usually seen as the lesser of the two evils, while YHVH, or the Great Will as he's been called since Nocturne, is just too evil to side with. Then Shin Megami Tensei IV: Apocalypse happened. No, YHVH is still evil. However, the Great Will turns out to be a separate entity from YHVH who has actively been trying to stop YHVH by creating Messiahs, effectively redeeming the Great Will.
- Bioshock Infinite: Burial at Sea reveals that Daisy Fitzroy was all along an agent of the Lucete Twins, and her Moral Event Horizon crossing and subsequent death at Elizabeth's hands were all part of the plan to harden Elizabeth and turn her into the woman who would in the future bring down Comstock and the Founders.
- In El Goonish Shive, Grace's brothers are of the "coerced/threatened" variety, since they are ruled by the iron fist of their powerful and abusive guardian, Damien. When Hedge kidnaps Elliot, he reveals that he's only doing it because he can't find Grace, and because Damien said he would kill him if he didn't bring someone back. He also gets hit by Damien for lying to him and disobeying orders. When Elliot's friends arrive to save him, Hedge tries to make them to leave before Damien finds out they're there. The worst thing Guineas does is guard Elliot, and his way of participating in the fight with Elliot's friends is by having a thumb war with one of them. Vlad initially appears to be at least somewhat sympathetic to Damien's mindset: He is confrontational towards Hedge, he willingly goes after Grace when he sees her arrive, and when Damien subdues her, he says, "I never like to see her hurt, but she brought it upon herself." He also is the one who alert's Damien to the presence of Elliot's friends, and ends up being the most vicious fighter against them. However, this all turns out to be a combination of lip-service to Damien and resentment for being unable to transform into a human.
- In Tribe Twelve we got Firebrand who at first was just a member of the slendy elite team AKA the Collective,but we soon learn that not only does he care about Noah but he is none other then Sir swear a lot himself. according to his own words he's always been there for Noah.
- In Worm, it is discovered that the Protectorate, and the Triumvirate, are being backed by the Nebulous Evil Organization Cauldron and its mysterious leaders. However, it turns out that Cauldron, and its [[nefarious deeds, like creating the mutated Case 53s and wiping their memories is actually the ones working to stop Scion from causing The End of the World as We Know It, and are just WellIntentioned Extremists who want to avoid a public panic, and possible the collapse of civiliation
- Hack & Slash of ReBoot only followed Megabyte's orders because they knew Bob would always stop them. When Bob is gone Slash can't bring himself to kill a Bi-Nome on Megabyte's orders, and says that he misses Bob. Then the two switch sides.
- One episode of Garfield and Friends showed that Jon had a pirate ancestor who seemed to be evil, but was in reality a spy for George Washington.
- Colossus in X-Men: Evolution was a member of Magneto's Acolytes. In his second appearance, it was revealed during a confrontation between him and Wolverine that he was a reluctant member of the group and Magneto had blackmailed him into joining. In subsequent appearances, Colossus was consistently portrayed as the most sympathetic member of the Acolytes and was the first to abandon the group after Magneto was seemingly killed by Apocalypse. He later helped the X-Men in their final battle against Apocalypse and was shown in the Distant Finale to become a full-fledged member of the X-Men following Apocalypse's defeat.
- In one episode of Tiny Toon Adventures, Plucky Duck who's often acts like a Jerkass is revealed to be a Jerk with a Heart of Gold. When Acme Looneversity was playing football against Perfecto Prep, Plucky seemed to be giving the opposing team's captain Roderick Rat the Looniversity playbook in exchange for transferring to Perfecto. When his number one fan Little Sneezer the mouse catches him talking to Roderick he tells Plucky "Say it ain't so, Plucky!". At the end during the last quarter of the game when Sneezer again tells Plucky "Say it ain't so, Plucky!", Plucky smiles and says "It ain't so, Sneezer.". Plucky and his team captain Buster Bunny immediately use a play together that was never in the Looniveristy team's playbook and when Roderick states so in angry confusion Buster tells him to check the back...Where Roderick finds the last page reading "Sucker". Turns out Buster planned to have Plucky pretend to help Roderick so they could beat his team in the end.