"As many people have noted throughout the years though, Disney has been rather...lax when it comes to adapting books and fairy tales into movies. This is understandable in some cases. Still, it can be a bit galling when one knows that the fire-breathing, demonic witch on the screen was a kindly old lady in the source material."
Fandom has a specific term for taking a character that is good (or neutral) and downgrading them to villain: Ron the Death Eater
Sonic the Comic – Online! does this with many games characters. Shadow, Rouge, the Babylon Rogues, Bean, Silver... even Cream the Rabbit! Blaze is immune to this, being almost identical to her game counterpart.
While Discord in canon was certainly malicious and powerful, he was presented more along the lines of a misbehaved brat than anything else, and the episode "Keep Calm and Flutter On" demonstrates that once he's exposed to The Power of Friendship he starts a friendship with Fluttershy and becomes an occasional helpful, if still jerkish, Trickster Mentor. However, many fan stories (most prominently the Pony POV Series and The Nuptialverse) present him as an unrepentant Ultimate Evil, responsible for multiple genocides and the Bigger Bad behind many other villains, among other crimes. This is somewhat more justified for fanfics that were written before "Keep Calm and Flutter On" and the character development Discord got in that episode; later works have less of an excuse.
While it's mostly Played for Laughs, Princess Celestia gets this a lot. There are memes of her being a tyrant who rules with an iron hoof and sends people to the moon at the slightest annoyance, a Discord-like prankster causing the cast's problems for the fun of it, or a Memetic Molester. Look up Tyrant Celestia, Trollestia, and Molestia, respectively. In Freedom Through Harmony, Celestia is corrupt and banished Luna for trying to reason with her. That still does stop her from becoming Nightmare Moon, though.
In Harmony's Warriors, a rather expansive crossover with the Marvel Cinematic Universe, many friendly side characters or background ponies are full villains, including Fancy Pants, Snowflake, Cheerilee, Carrot Cake, Fleur de Lis, Gustav, Hoity Toity, and Filthy Rich.
In the G1 special that he premiered in, Scorpan was a Nice Guy who happened to work for Big Bad Tirac, and in Friendship is Magic it's mentioned that Scorpan befriended the ponies and helped them imprison Tirek in Tartarus. The Warmistress of Equestria, however, portrays Scorpan as a manipulative, bloodthirsty Lord of Chaos whose Evil Plan is to break Tirac out of the Warp and sacrifice Equestria to the Dark Gods.
In the Alternate Universe Fic series The Dashverse, the canon villains become much more threatening. They aren't too monstrous that the series is grimdark, but they do sink to depths not approachable in canon.
In Rainbooms and Royalty, the re-imaging of the pilot, Nightmare Moon assaults and repeatedly tries to kill the Mane 6, especially Rainbow Dash, brainwashes Shining Armor and Ditzy Doo into her loyal minions, and threatened to drop the rest of the Mane 6 to their deaths and forcing Rainbow Dash to choose which ones to save. By the end, it is not surprising that Rainbow Dash hasn't forgiven Luna.
In Hot Heads, Cold Hearts, and Nerves of Steel, King Sombra, who was already a Crazy-Prepared and evil dictator in canon, kidnaps the foals of Ponyville and brings them to the Frozen North. When Rainbow Dash reaches his lair he enters Rainbow's head and tells him his backstory: he started out as just as snobbish prince before he obtained the Alicorn Amulet. Afterwards, he sought even greater power, he murdered his wife, manipulated Luna into falling in love with him, and even after his defeat by the Princesses, he knew he had driven Luna into the despair that would create Nightmare Moon. He then reveals his plan, to sacrifice the foals to increase his power and become an alicorn god. And he comes pretty damn close as well.
Moonstuck is a weird case, as while Discord is just as nasty as his canon self with the same personality and powers, the comedic traits of the former are strongly downplayed while the latter are played up to almost Eldritch Abomination levels, and the fact that he's doing all this to a child makes his usual antics ten times worse. The character design also helps; while his canon goofy Mix And Match Critter appearance makes him hard to take seriously sometimes, in Moonstuck he's drawn in a monochrome, overbearing, heavily sketchy style reminiscent of the Anti-Spirals.
In the fanfiction Sunset Of Time, the Big Bad Vesper Radiance is a re-imagining of a canon antagonist. For it, she's not only far worse than she was in the canon, she's worse than any of the other villains too. She's ambitious, hungry for power, casually murders (or attempts to murder) several characters, and her ultimate goal is to become a Physical God to rule over Equestria — after killing off all three Princesses, Twilight and her friends, and anyone else who dares try to stop her.
Damion, a one-shot character from Pokémon, was originally just a Jerkass becomes a dangerous psychopath in Symbiosis. He is willing to kill Ash to get revenge on Brock and Misty for reporting his crime.
In The Simpsons AU The Fourth Simpson Child, Lisa goes from a socially isolated smart girl who is somewhat The Unfavourite to a Smug Snake who is openly jealous of Samantha (her older sister and the title character).
Wriggle is just a run-of-the-mill insect youkai and, while still dangerous, she usually has no malicious intentions against humans and will attack only if provoked. In the fanfic No Such Thing as Fairy Tales, Wriggle is a fae, who spirits aways humans and torture and rape them for no other reason because she can.
Touhou Ibunshu does this to almost half of the cast. Rumia, Mystia, and Remilia are Creepy Children that eat people, Cirno, Wriggle and Hina are sadists that try to kill people for no reason, Sakuya is a Serial Killer and succeeds in killing the humans, and Yukari and Mokou both try to obliterate Gensokyo. Strangely, the ones that get some Character Development end up being more sympathetic than the originals (most of whom are petty violent jerks), even if they are worse people overall.
Imperfect Metamorphosis takes Yuuka Kazami (a powerful and dangerous individual who nonetheless mostly leaves people alone) and turns her into The Dreaded who makes every character crap their pants whenever she's mentioned, and more than lives up to her reputation by being a full-blown Outer God.
In I'm Here to Help, the senshi of the future, as well as Neo-Queen Serenity, are portrayed as considerably more villainous than their canon counterparts. While we don't see much of them, it's established that they are essentially the Big Good of the future, to the point where they were willingly asked to rule the now-united Earth. In the fanfiction though, their adoration comes from Neo-Queen Serenity "purifying" all negative emotions out of them, allegedly turning them into placid zombies. While Emerald is something of an Unreliable Narrator due to being insane, one segment told from the point of view of the future Jupiter and Mars has them discuss how they attacked/killed several children who Emerald had help with one of his plans, dismissing the whole thing as the children having made their own choices in the matter. Needless to say, the canon senshi would never willingly harm children, whether or not they were helping a villain.
The first and second victims, while acting similarly to how they did in canon (hoping to kick-start the mutual killing and planning a murder so that Kuzuryuu can gradaute, respectively), they come off as somewhat less sympathetic, since their motives are revealed after their deaths.
The second murderer, and the first who's different than canon, is Sonia Nevermind, who not only never killed anyone in canon, but was also one of the nicer cast members.
In the MLP / Green Lantern crossover In Brightest Day while Mitta and Ruby were in fact friendly and helpful towards Apple Bloom. However in this story while Ruby feels constant remorse and guilt for her horrific actions, Mitta seems to be completely villainous and relishing in the pain and suffering of her victims. The reason of this has yet to be explained...
Utakata, Yagura and Gaara are the three most villainous members of the Kyuushingai introduced, with Utakata being an Ax-CrazySerial Killer who'll even murder children in his rampages, Yagura being a cold-blooded gang leader who's infamous for making witnesses set to testify against him "disappear", and Gaara being an aspiring drug kingpin who's in an alliance with Yagura. Contrast their canon counterparts from Naruto, where Utakata was merely disillusioned after being mistreated due to his jinchuriki status but wasn't otherwise stated to be evil, Yagura only had his bad reputation because he was manipulated into committing bloody actions during his time as the Mizukage, and Gaara is one of Naruto's staunchest friends and allies (though he did start out Ax-Crazy and only wound up undergoing a Heel-Face Turn following being defeated in combat by Naruto).
Konan is a member of Akatsuki and determined to kill the Kyuushingai no matter what (in canon, she's also a member of Akatsuki, but there she's a Well-Intentioned Extremist who later becomes one of Naruto's supporters).
In canon, Tsukune's ghoul form was largely depicted as an instinctive, mindless Berserker. Here, it's shown as a full-fledged Superpowered Evil Side with its own identity and personality.
Though Hokuto was always an antagonist in the manga, he was more of a Wild Card to the extent that he helped Tsukune and Moka stop his own plan. Here, he's a straight-up no-gray-area villain and a blatant Straw Nihilist who openly expresses the view that life itself is nothing but a meaningless plague that must be wiped out.
In Necessary To Win, Anchovy of Anzio is based off of her manga counterpart, and as such, is a Sore Loser who criticizes Miho's decision to save one of her school's tanks at the cost of winning the tournament. On the other hand, she does go through some Character Development and gains respect for Oarai, unlike in the manga.
Danganronpa Abridged Thing does this to the first murderer. In canon, the crime was committed in what was arguably self-defense, although it's pointed out that the killer technically went out of his way to get to and finish off the victim. In the abridged series, the murderer accepted the victim's invitation, hoping to "get some," and killed her when she called him a "weenie."
TNG Recut, The Abridged Series of Star Trek: The Next Generation, turns the entire crew of the Enterprise-D into a bunch of crazed nutcases. Picard takes the cake, though, ultimately leading his crew to strand him on the saucer section and launch it into a planet to get rid of him. And even then it doesn't work!
Mr. Popo. In the original show, he was a kind, peaceful man who helped the protagonists. In this version, he is a rude, sadistic and intimidating bully who all the main characters fear. He puts his students through hellish training for the fun of breaking them, is implied to be a rapist, has a magic carpet fueled by souls (suggesting he kills people for their souls), plots to destroy the world with Shenron, and Kami states that the last time Mr. Popo kicked him off the lookout, when he came back "I found five corpses. He laughed when I said five".
Guru. Unlike the kind grandfather like figure he was in the actual series, here he caused a huge drought that nearly whipped out the Namekian race, blamed the Albino Namekians for it, and ordered their genocide. He also orders Nail to murder Krillin, and sends Nail to fight a battle with Freeza knowing he stands no chance. When the heroes summon the dragon, Guru dies on purpose and ruins everything just to be a dick. Guru also laughs when he hears that Vegeta slaughtered a Namekian village. In the Lord Slug movie, it was revealed that he was Slug's evil half, and that he suggested to Slug that he attack Earth in the first place, telling him that their defenses suck.
Ms. Maia from Twilight Valley. In the sixth The Land Before Time movie, she is simply an overprotective mother that tossed out Ducky when Ducky was the one who invaded her nest in the first place. In the fanfic, Ms. Maia is portrayed as a traitor who attempts to murder Ducky.
In the original story of Saint George and the Dragon and most reworkings of it, Saint George is the hero. For example, in The Reluctant Dragon, he becomes the title character's friend. Even in retellings where the dragon is Spared by the Adaptation, George usually convinces it to Heel-Face Turn. In the Dragon Keepers series by Kate Kilmo, Saint George is a Villain with Good Publicity who enslaves magical creatures and drinks dragons' blood while the princess he saved is an evil witch. The dragon from the original tale tells his own side of the story, in which he was a benevolent sorcerer betrayed and killed by George.
Myth-O-Mania has some in-universe examples: When Zeus rewrote the stories of Classical Mythology, he exaggerated monsters' scariness to glorify the heroes. (eg, The Minotaur went from being a vegetarian to eating humans.) Plus, Zeus claimed that Hades kidnapped Persephone, when actually she hitched a ride on his chariot while running away from her overprotective mother.
The mice from The Hitchhiker's Guide to the Galaxy — in the radio play, they are fairly amiable, and upon discovering that Arthur is in the ideal position to find the ultimate question, offer to make him "a reasonably rich man" if he does. In the book and subsequent adaptations, however, they are much more sinister, plotting to steal his brain in order to read the question from it.
Likewise, the Wizard is not necessarily a good guy, and does several reprehensible things, but when Greg Maguire got his hands on Oz for Wicked, the Wizard became a power-seeking, first-rate Magnificent Bastard who exploits religious factionalism and Fantastic Racism to pit his potential enemies against one another, drive Oz into civil war, and start genocide of the sentient beastsas a cover for him trying to locate the Grimmerie and obtain absolute power.
The Queen of Hearts is clearly a mean woman and a blustering Jerkass type, but calling her evil might be stretching the definition a little; though she often calls for people to be beheaded, her husband secretly pardons most of the people she condemns, and the Griffon tells Alice that, "It's all in [the Queen's] fancy, you know. They don't actually execute anyone." Nonetheless, you can be sure in almost any modern story where Alice is portrayed as the protagonist, the Queen of Hearts (often conflated with the Red Queen) will be the villain, and portrayed as far more evil than Carroll could have ever imagined. Whereas Alice's trial in the book ends with her realizing that the Queen of Hearts' threat against her is empty and dismissing the Queen's court as a pack of playing cards, in the 1951 Disney version, the Queen of Hearts is portrayed as a genuine threat, and the trial ends with Alice running for her life from the Queen and her soldiers before waking up.
The Jabberwock is often both this and an Ascended Extra in such works, seeing as the evil beast wasn't even an antagonist for Alice in Through the Looking-Glass, only appearing in the now-famous poem that she read. The poem became so popular that most modern adaptations include the creature as an adversary for Alice and the heroes in general.
In the picture book The Butterfly Ball, Sir Maximus Mouse, the cheese tycoon, is simply a workaholic who's too busy to go to the Ball. In Roger Glover's concept album adaptation, he's a borderline-demonic Corrupt Corporate Executive.
Aside from a fight when she premiered in one issue of the Comic Book, the Black Widow has never been a Spider-Man villain. Yet Gottlieb's The Amazing Spider-Man pinball has her on the backglass along with Spidey's other rogues, such as the Vulture and the Green Goblin.
This happens to several characters in Love Never Dies, the sequel to The Phantom Ofthe Opera. The trope applies in two ways, both because characters from the first musical undergo villain transformations and because in The Phantom of Manhattan (the Frederick Forsyth novel that was the result of early work on what became this show) contains no such transformation, instead having the villain be a completely new character who didn't make it to the stage. Madame Giry is more-or-less the main antagonist, and only helps the Phantom for the reward it earns her. Meg gradually loses her sanity while trying to start a relationship with the Phantom, culminating in her kidnapping and attempting to drown Gustave, then ultimately shooting Christine. Meanwhile, more adaptational Jerkass than villainy, but Raoul is now a cranky alcoholic whose gambling has put the family in a load of debt, and no longer feels the love for Christine that he once did.
In Wonderland: Alice's New Musical Adventure, the Mad Hatter becomes female and the play's main antagonist, with the March Hare as her Dragon. In the book, he's scatterbrained, but not particularly malicious about it.
In The Golden Ticket, an opera adaptation of Charlie and the Chocolate Factory, Spoiled Brat Veruca Salt agrees to a deal with a TV reporter to secretly film and photograph the titular, top-secret factory during the Golden Ticket tour — which makes her and her dad, who goes along with the plan, spies. As well, she's much nastier in her selfishness than in other versions, and specifically contrasted with poor-but-good Charlie Bucket throughout. With this in mind, while the novel and all other adaptations have them the third group to be eliminated from the tour, here they're the fourth and last to go.
When it comes to other characters, the extras actually contain a spectacular Inversion. One strip features a man who stuffs minus in a briefcase after luring her in with promise of sidewalk chalk, and who would certainly have tried to abduct her if he wasn't stopped. His counterpart in the extras, on the other hand, is an innocent bystander who doesn't do anything to deserve being antagonized by the villainized minus.
Darths & Droids does this to Han Solo, who shortly before being frozen in carbo... er, alcohol, admits he's been feeding information the the Empire for months. Jim was really impressed with how Annie roleplayed Anakin's Start of Darkness and wanted to do the same.
This page lists five well-known characters who were reimagined into villains through Disney movies in this way.
The Day of the Barney Trilogy takes Barney and Baby Bop, who are portrayed as sincere and good friends to the kids on Barney & Friends, and portrays them as villains who successfully get the world's children to kill any adult they come across, kill their male Special Friends when they turn thirteen, and take the thirteen year old girls away to fatally mother mutated offspring. They're even revealed to be Really 65 Million Years Old and to have been the harbringers of many of the world's evil dictators and catastrophes.
Hilariously, the Lighter and Softer version of the game Warhammer 40,000, Brighthammer 40000, does this to the Tau Empire. To explain, Warhammer 40000 is an extremelygrimdark setting, with a number of genocidal, xenocidal and one or two omnicidal factions locked in a Forever War. The sole exception is the Tau, who are still bad in a sense but one of the more sane, if totally unsympathetic, factions. For Brighthammer 40000, every faction except the Tau have been made more sympathetic, while the sinister aspects of the Tau have been played Up to Eleven, along with some new ones added. This has the effect of turning the Tau into the setting's Big Bad. Water Caste Tau are all conniving schemers and cheating merchants, Air Caste Tau are all cowards who launch unprovoked bombing runs and orbital strikes on defenceless worlds, Fire Caste Tau are all violent brutes who bully other Tau and use prisoners of war for target practice (when they bother to take prisoners at all), and the Ethereals run the empire as this horrible 1984-esque society and often use mind-control to order Tau to kill themselves, sometimes for fun. Only the Earth Caste escape this treatment, being poor schmucks who are abused, exploited and left to die when they're no longer useful.
The Midwestern Brotherhood of Steel are just downright fascist in one of the worlds from We Are Our Avatars, they even tortured an Enclave soldier even though he's a Punch Clock Villain.
In Noob, the novel and comic versions of Donteuil in regards to the webseries one. When that fact that Fantöm's avatar was illegally enhanced get revealed, Judge Dead is the one who decides to blame the whole thing on its Locked Out of the Loop victim. A couple of scenes give the impression that Donteuil has a My God, What Have I Done? feeling towards the victim in question and it's via Donteuil that the audience eventually finds out that the victims situation isn't as bad as it first looked. In the novels and comics, Donteuil seems to be the one who decided to pull the "blame the victim" move, while the "situation not as bad as it first looked" reveal comes from a Fictional Document provided by another character that gets no mention in the webseries.