In the comics, "Deathlok" referred to multiple characters, all of which were heroes. In the show, "the" Deathlok is a basically good person but Trapped in Villainy. "Ragtag" also reveals that the original Deathlok is also The Clairvoyant, the Season 1 Big Bad.
The Clairvoyant is ultimately revealed to be Agent John Garrett, a loyal S.H.I.E.L.D. agent in the comics. This ties in with Captain America: The Winter Soldier, where some agents who were good in the comics are part of the Hydra infiltration of SHIELD. Just like the heroes themselves, the audience no longer knows who to trust.
The episode "Dodger" turns a Loveable Rogue from the comics into a ruthless and calculating killer.
Eddie Feyers in the comic was a shady character but basically an ally to Green Arrow, as long as his CIA bosses didn't say otherwise. After Ollie's death, he even became a Parental Substitute to Conner Hawke. His live action counterpart is the Big Bad of the Season One island flashbacks.
"Blast Radius" introduces Shrapnel as a Mad Bomber, which is a reasonable depowered version of the character. The adaptational villainy comes in when the group he's part of - which is identified because they regularly use that kind of bomb in their terrorist activities - is called The Movement.
Helena Bertinelli, AKA the Huntress, is also changed from a brutal Anti-Hero (think Batman without any issue with killing) with a strict moral code into an Anti-Villain who carelessly kills innocents to get revenge on her father. She seems to be getting better by the second season, choosing to spare a few people she could have easily killed, though still threatens to kill hostages, and at the end realizes how pointless her revenge scheme was.
Helena's father Frank Bertinelli is also far more villainous; in the comics, Franco Bertinelli was a mobster still, but one who seemed to genuinely love Helena before he was murdered by her biological father, resulting in her becoming Huntress to avenge his, and the rest of her family's deaths. The show however has him as the object of her vendetta, for killing her beloved fiancé, and once he finds out she's trying to kill him he sees no problem in trying to blow her brains out the first chance he gets. Like above, the Second Season has him genuinely remorseful for being the one who turned his daughter like this and willingly accepts the fact she's going to kill him, hoping it'll stop her warpath.
Captain Cold in the comics was one of of The Flash's more nobler enemies, refusing to murder innocent people and displayed a great amount of respect for the scarlet speedster himself. This incarnation is a cold blooded crook who endangers civilians, and even killed one, and doesn't mind property damage or kidnapping to get the job done. After learning Flash's real name though, the two strike a deal. He agrees not to reveal Flash's identity and not endanger civilians so long as Barry doesn't leave him in the pipeline, likely meant he's starting to act more like his original counterpart.
Hartley Rathaway/Pied Piper, was one of the first of the Flash's villains to have a Heel–Face Turn in the comics, and the only one where it stuck. In the series, he's one of the most ruthless and calculating villains Barry's faced.
In the comics Lashawn Baez/Peek-A-Boo is an Anti-Villain who was trying to steal a kidney to help her sick father, and at one point tells the Flash that she wanted to be a superhero. In the series, she was already a petty criminal when her powers manifested and seems to be a lot more ruthless. While it could still be argued that a difficult situation has forced her into becoming a Flash Rogue, the narrative is less on her side.
The original Trickster was another Flash villain better known for his Heel–Face Turn, and even as a villian he was never a particularly homicidal one. The TV version is a mass murderer (as he was in The Flash (1990), since he's played by Mark Hamill as basically the same guy).
In the comics, Zoom was the identity of Hunter Zolomon, who was a villain in order to make The Flash, then Wally West, a better hero. While that might not be his identity here, the Big Bad of the season 2 who goes by Zoom is a frightening monster who is out to kill all people with super speed to make sure he's the only speedster in the multiverse.
From Dusk Till Dawn: This happens to Carlos. In the original movie he was merely the brothers’ contact in Mexico and unaware of the Titty Twister’s true nature. In the series he’s a full blown vampire.
Littlefinger is a lot less subtle in the series than in the books. The book version makes a game of looking like The Trickster who is snarky but generally harmless (though he's actually anything but). The live-action version is a Devil in Plain Sight who's openly feuding with The Spymaster of the series. Furthermore, in the books, he isn't involved in anything so vile as serving up his prostitutes to necrophiliacs and serial killers.
Doreah does a Face–Heel Turn in the show that was not in the original books. This is probably because she simply dies of illness in the books, so the show gives her a more eventful demise.
The character Dagmer Cleftjaw was written out of whole cloth for the series. In the books, he's an Honorary Uncle for Theon Greyjoy, and sticks up for him. All in all, he's a fairly decent guy, at least by the standardsof theIronborn. In the series, he's an Evil Mentor who seems set to guide Theon to alienate himself from the Northmen he grew up with, corrupting Theon as much as possible, and then sells Theon out when it's a choice between that and dying in a blaze of glory.
In the show, Stannis Baratheon is made more morally grey by being much less concerned about the prospect of sacrificing innocents in magical rituals to secure his throne. He also physically assaults Melisandre at one point. And then he sacrifices his daughter by burning her alive to gain the favor of the Lord of Fire, essentially making all his pretenses to justice go to hell. Melisandre and Selyse are also considerably more pro-burning alive than in the books.
Rast is a rapist and a Jerkass in the books too, but he never betrays the Night's Watch, and dies defending Castle Black against wildlings. In the show he stabs Lord Mormont to death himself, and reluctantly sacrifices an infant to the White Walkers before being killed by Ghost.
In the books, Xaro Xhoan Daxos wants nothing more than to marry Dany so he can get control of one of her dragons, but in the show he allies with the warlocks to assassinate the rest of the Thirteen and seize control of the city, then imprison Daenerys and steal all of the dragons.
Joffrey is a horrific power-crazed psychopath in the books, but his show counterpart's taste for sexual violence against prostitutes is an exaggeration (or perhaps an extrapolation, given his age-up) of his sadistic streak. He also treats Cersei far worse, and two of Cersei's biggest Kick the Dog moments in the books are done by him instead.
Jaime gets extra villainous actions than he had in the book, including murdering a member of his house whilst imprisoned by Robb. In Season 4, his sex scene with Cersei is considerably more forceful than that described in the book, causing many viewers to regard it as rape.
In the books, the Thenns are more traditionally civilized than other Wildlings, characterized by their higher technology and greater respect for authority. In the show, they're changed into a group of scarred up, gleefully sadistic cannibals that disgust even the other Wildling raiders.
The book version of Ellaria Sand is actually the voice of reason in Dorne and tries to dissuade her stepdaughters from diving into the Cycle of Revenge, arguing that it wouldn't bring Oberyn back. In the show she is their commander in this operation and goes as far as killing an innocent young girl just because she's a Lannister; and betraying the vow of obedience she's made to Doran.
In the books, Meryn Trant is certainly the most vile of the Kingsguard, being one of the guards who has no qualms about beating Sansa. The show's version of Ser Meryn essentially combines him with Boros Blount. The series made him even more villainous, by revealing that he's a sadistic ephebophile who likes to beat young prostitutes before having his way with them. Arya disguises herself as a prostitute and lures him into a trap before killing him. In the books, it was Raff the Sweetling who she seduced and murdered.
In the comics, Sarah Essen was a clean cop, but here, she's a reluctant Dirty Cop.
Penguin is more willing to commit bloodshed than other incarnations.
The character of Gerald Crane is a murderous Serial Killer, while in the comics he was a civilian whose worst crime was abandoning his pregnant girlfriend Karen and their unborn son, Jonathan. This is largely because the show borrows more heavily from his characterization in the New 52, in which he is a Mad Scientist who, unlike his TV counterpart, experiments on his son for no reason whatsoever beyond For Science!.
Although she isn't a full blown villain, Barbara Kean isn't quite as nice as she is in the comics. She willingly cheats on Gordon with Montoya (and eventually, the Ogre), and tries to convince Selina that she could use her beauty as a weapon. But perhaps the most striking instance occurs in "Under the Knife", where she begins to establish a firm relationship with the Ogre. When he introduces her to his secret torture room, she isn't the least bit disturbed. In fact, she smiles at him. She's embraced this trope by the season one finale, having killed her own parents and trying to kill Leslie Thompkins.
Justified: Raylan's father, Arlo Givens, is a ruthless Manipulative Bastard and lifelong criminal with few redeeming qualities. In the original books he was a coal miner who died of black lung when Raylan was still a teenager.
Kamen Rider Fourze does this in a couple of its Movies, which adapt characters from other Shotaro Ishinomori shows. In Everyone, it's Space Time!, the villains are based off of the Space Ironmen Kyodain, while in Movie Wars Ultimatum they're based off of the Akumaizer3. For a bonus, the former also inverts this trope by featuring heroic characters based off of Kyodain villains Black Knight and Goblin Queen (though with her it's sneaky; the name Inga Blink is a Significant Anagram in Japanese; the katakana easily rearranges from Inga Burinku to Gaburin Kuin by moving one character from the end to the beginning; we're basically talking Pig Latin.
Lois and Clark: Mr. Mxyzptlk received this treatment. He was a superpowered imp from the 5th dimension like in the comics, but rather than the relatively harmless trickster as he usually is, here he's a Faux Affably Evil villain who traps the world in a time loop where each time around humanity grows more depressed and pessimistic to make them all cross the Despair Event Horizon and destroy themselves.
The Genie from Aladdin. Here, he falls in love with Regina (who is married to King Leopold), and eventually murders him to free Regina from what he believes to be a loveless marriage, unaware that Regina has manipulated him the whole time. Even after learning the truth, he remains madly in love with her, and uses one of his own wishes to always look upon Regina's face, resulting in him becoming trapped in her mirrors (making him a composite of the Genie and the Magic Mirror from Snow White).
Jack the Giant Killer is re-imagined as a selfish treasure hunter who took advantage of a naive and good-hearted giant. However, this is actually an example of an Unbuilt Trope concerning a different folk tale. Jack and the beanstalk is a separate myth from Jack the Giant Killer. Jack from the latter is the hero portrayed in most modern adaptations (though he never ascended a beanstalk) while Jack from the former is considered by some to be a Villain Protagonist who is a petty thief and liar - much like the "hero" proposed in this series. In an interesting twist from the show's formula, audience expectations are slammed by having a character portrayed as s/he was in the original myth, rather than complete deviation.
Regina's abusive and ruthless mother Cora is a Composite Character of the Miller's daughter and the Queen of Hearts. The former was a sympathetic heroin and the latter was Played for Laughs.
They did a really big twist by turning Peter Pan and most of the Lost Boys into the villains. Word Of God says they decided to do this because they thought about how messed up a person would have to be if they wanted to remain a kid forever. Interestingly enough, Captain Hook, one of the show's villains, redeemed himself at the end of the second season where Pan is revealed to be the Greater Scope Evil of one of the Season 2 villains and eventually the first Big Bad of Season 3.
Season 4 turns Little Bo Peep into a villain of the week, making her a witch warlord who turns people into her "sheep" by enslaving them with magic if they can't pay their debts to her.
All twelve of Hans' brothers are minor antagonists, while they were neutral characters in 'Frozen. While the behavior of at least some of them towards Hans contributed to his villainy (according to Word Of God), they were never directly antagonistic towards Anna and Elsa, and his scheme took place without their knowledge or approval. In the series, they attack Arendelle under his leadership.
Season 5 also has the sons of the clan chieftains in Brave, now chieftains themselves. In the film they start out as annoyances to Merida (mostly at the badgering of their fathers) and end up as friends when they accept she has no intention of being betrothed to them. In the series, they're prepared to kill her brothers to force the issue.
Once Upon a Time in Wonderland turns the Caterpillar into a villain; he was a side character who gave cryptic advice in Alice in Wonderland, but turns out to be more like a mob boss in the series. (Then there's Jafar, who was evil to begin with and got worse.)
Prince Wars Gill in Kaizoku Sentai Gokaiger was an Affably Evil spoiled prince that often felt disappointed and woeful whenever his schemes against the Gokaigers failed. In Power Rangers Super Megaforce; Prince Vekar has his petulant qualities largely downplayed and focused more on conquest against the earth and the Power Rangers. His father is rendered in a similar manner: whereas Emperor Akudose Gill was taking over the Zangyack invasion because of disappointment from his son's failures; Emperor Mavro is far more vengeful of his son's defeat, making his desire to defeat the Power Rangers with the Armada more malevolent.
Sharpe: The television adaptation of the novel Sharpe's Battle was written before the novel had been finished, resulting in a vastly different second half. So while Lord Kiely gets a much more sympathetic treatment in the adaptation and dies a heroic death (rather than blowing his brains out on realising he's a bit rubbish), Spear Carrier Guardsman O'Rourke, whose main contribution in the novel is to say his name when Sharpe asks him, gets turned into a Turn Coat who kills a couple of likeable characters mostly because they're there.
This happened to Salem in Sabrina the Teenage Witch. When Sabrina first appeared in Archie Comics, Salem was little more than a pet cat who occasionally had human thoughts. The series changed him into a more active character, and made him a once-human warlock who had been transformed into a cat as punishment for attempted world conquest. While not a true villain on the show (most of the time) he's usually the resident Jerkass.
Sherlock: In the original story Irene Adler has an incriminating picture of herself with the King of Bohemia which she has not intention of using, and keeps as protection against him. In the show she has multiple pictures of various important people she keeps as insurance, but also hands top secret counter-terrorism information to Moriarty, and blackmails the British government with the photos for millions of pounds to satisfy her own power fantasy.
Sleepy Hollow: In The Legend of Sleepy Hollow, Abraham is the local hero who played a prank on the obnoxious Ichabod Crane by pretending to be the Headless Horseman. The show's version of Abraham is the Headless Horseman, with downright murderous intentions for Crane.
This version of Bizarro is less of a Harmless Villain and more of a dangerously intelligent one.
Mr. Mxyzptlk isn't a funny omnipotent imp, but more of a smug psychopath who likes to use his Mind Control to induce Squick and tries to stab Chloe for a deal with Lex Luthor.
Lana Lang is also turned into a much shadier character, although that may well have been unintentional; the show's creators seemed to think she was all but a Purity Sue to the very end.
The comic book incarnation of Zor-El sent his daughter, Kara, to Earth as a protector for her cousin, though at one point he was wrongly believed to have been a villain who sent his daughter as an assassin. The series made him an outright villain who sent his daughter to Earth as part of a plot to have himself resurrected as a conqueror.
Supergirl's Starter Villain is Vartox, who in the comics was a hero and occasional associate of Superman.
Jemm, Son of Saturn, appears in a later episode as a would-be conqueror. In the comics he's a pacifist hero. He was in opposition to Superman during the New Krypton storyline, but it was more complicated than him being a villain.
Super Gran: In Forrest Wilson's books, the character Tub, while initially a somewhat reluctant henchman to Campbell, becomes a good guy in later books following a Heel–Face Turn. In the TV show, he is a Card-Carrying Villain who goes along with Campbell's plans unquestioningly.
Stargate SG-1 does this to nearly every polytheistic pantheon, as the Goa'uld are Always Chaotic Evil and named after (or inspired; it's never made clear) most early human religions. The most obvious example is Anubis, the most evil Goa'uld by a huge margin who shares a name with a good god in Egyptian Mythology.
The real villain isn't the Affably Evil Silver; it's Squire Trelawney, who plots to cheat Jim and Dr Livesey out of their share of the treasure, arranges for Mrs. Hawkins to be thrown out of the inn while they're away, has Mr. Arrow executed, and eventually suffers a Karmic Death by diving after the treasure when Jim throws it overboard. Not much like the excitable but well-meaning "most liberal of men" in the book.
Tom Redruth, Trelawney's gamekeeper, gets this, too - in the book, he is an elderly man who accompanies Trelawney to the island and is killed by the mutineers. In the series, he is Trelawney's vicious enforcer back in England.
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