Most Yu-Gi-Oh! villains don't rise above literal Card-Carrying Villainy, with some being in the Anti-Villain or Woobie, Destroyer of Worlds territories. But there are a few that are just plain nightmarishly evil to the core.
- Yu-Gi-Oh! gives us Dark Marik, the twisted Split Personality born of abuse, darkness, and rage who drove the real Marik off the deep end in the first place. Seizing control of Marik's body during his childhood, he killed their Abusive Dad, then tried to kill their adoptive brother, who had been keeping Dark Marik locked up. This failed, and Dark Marik bided his time, gaining strength, and driving Marik to further and further acts of cruelty in his quest to Take Over the World. Resurfacing as an Enemy Without when Marik's brother was defeated in the Battle City semifinals, Dark Marik exiled his better half from their shared body, then engaged Mai Valentine, The Spirit of the Millennium Ring (not a saint himself as you read below), and Joey Wheeler in a series of increasingly sadistic Shadow games that saw all three damned to the Shadow Realm. He also made several attempts on the lives of his sister and comatose adoptive brother. This all culminated in a final battle against Yami, during which he arranged for any damage the two of them incurred to be suffered by their better halves, Marik and Yugi, nearly killing them both. An Ax Crazy Combat Sadomasochist with omnicidal designs on the world, Dark Marik left the cast in shell-shock and irrevocably altered the tone of the series from that point onward.
- The Spirit of the Millennium Ring, better known as Dark Bakura, was the show's longest running antagonist, and one of its worst, possessing Yugi's friend Bakura for almost the entire duration of the series. During the Duelist Kingdom arc he traps Yugi and his friends within the card game, resulting in their being sent the graveyard if defeated. He subsequently tries to bodyjack Mokuba Kaiba, and rips Pegasus' Millennium Eye out of his eye socket, leaving him in a coma. (In the manga, killing him). During Battle City, he infiltrates the tournament and sends Bonz, Zygor, and Sid to the Shadow Realm for eternity, then tries to do the same to Yugi and Yami. He arguably doesn't quite cross the line into this trope until he returns in Season 5 as The Big Bad. Outing himself as an agent of Zorc Necrophades, the Spirit of the Ring repossesses Bakura, and sets in motion a plot to bring about the end of the world as we know it. He kidnaps Mokuba to force Kaiba into a Shadow game, then traps the entire cast in the Memory World, where he can control their lives, possessing Tristan and his own past self, Thief King Bakura, in the process. Eventually pulling a You Have Outlived Your Usefulness on his own past self, Dark Bakura unleashes Zorc in the past, while taking on Yami in his final Shadow game in the present, with the intent of making the entire world bow down to his dark god. It's revealed that the Spirit's agency is not of his past self, but of Zorc himself since a fragment of Zorc's soul resided in the Ring the Thief King's spirit was sealed in.
- The anime-only Doma arc featured a Big Bad named Dartz, formerly the king of Atlantis. While at first he was obeying the stones of Orichalcos in hopes of saving his civilization, being told to summon the Great Leviathan that could destroy the world and re-create it free of the corruption that had swept Atlantis, Dartz soon fully embraced the stones corrupting influence and led his civilization to it's destruction instead. Leading an army of undead beastial warriors, he fought against the three guardian dragons in the battle that led to Atlantis' sinking. He also gave the dragon Timaeus it's scar, and he's also implied to have killed his own father and daughter. Living for centuries under the influence of Orichalchos, Dartz grew to resent the entire planet and see human beings as wicked beings in need of eradication. Now completely far gone from his well-intentioned roots, he plotted to revive the Great Leviathan in order to raze the world and wipe out humanity, after which he could create a new world order where he'd have control of the souls of all that lived. Human souls were also required to revive the Leviathan, so Dartz started harvesting souls as he worked on his Evil Plan for 10,000 years. Aside from mass soul stealing, his crimes included corrupting players of Duel Monsters with the Seal of Orichalcos so that their souls were susceptible to being taken away, war profiteering under the guise of Gozaburo Kaiba and causing the deaths of several innocent casualties including Alaister's little brother (all so that Alaister could join him), sinking a ship full of people including Raphael's family (so that Raphael could join him), burning down a nunnery and killing everyone inside including Valon's caretakers (so that Valon could join him), many attempts at murdering Yugi and his friends, and sacrificing his own self to merge with the Leviathan and complete his efforts that put the entire world at great risk. While his soul ended up cleansed and redeemed after he and the Leviathan are destroyed, Dartz was shown to be hopelessly lost in his self-righteous delusions and malice while he was alive. He was such a monster that he could only ever find any sort of redemption after he was already dead.
- Brron, Mad King of the Dark World of Yu-Gi-Oh! GX, is demented and sadistic, ruling the Spirit World as it's vile dictator and being responsible for it's deplorable state and oppression of its denizens. His right-hand man, Zure, oversaw Brron's will, detaining anyone who defied him in internment camps while killing duelists who could be threats to him. The executions occurred at his fortress and involved releasing monsters at disarmed duelists while Brron himself and his minions watched the spectacle. After learning of Jaden's presence in his domain, Brron orchestrated a plot that involved turning Jaden evil by sacrificing all of his friends one by one with his set of "Wicked Doctrine" cards to create the "Super Fusion" card. After his defeat, Brron mocked Jaden by saying that he would never see his friends again before dying.
- Tragoedia, the manga exclusive Big Bad, was formerly a human from the village of Kul Ena. After it was massacred, Tragoedia was trialed by the malice inside of his heart, resulting into him becoming a ka. After he tries and fails to kill the priests, he's sealed away for thousands of years. When he's uncovered, Tragoedia has his spirit either possess or corrupt duelists to duel others in pain inducing shadow games where the loser will be trapped in a dimension of darkness for eternity. He gives Koyo Hibiki a special punishment, where his life will slowly and painfully deplete with every passing duel Koyo has for the sheer fun of Koyo being harmed by what he loves doing. While possessing Principal Mackenzie, Tragoedia manipulates the american students into draining the energy of other students to fuel to restore his body, only to drain their life energy when they've fulfilled his purpose. Once Jaden and Chazz confront him, he reveals that the only reason he sent hundreds of people into the dimension of darkness was to kill his boredom throwing away any possible sympathy for him about his village being massacred. He then duels the two for the sole reason of seeing them in pain during their shadow duel. Tragoedia's a sadist who only takes pleasure in causing people suffering.
- In Yu-Gi-Oh! 5D's, Divine/Sayer is the leader of a group of duelists training to control and harness their psychic abilities in order to turn them into soldiers of war against the rest of humanity. His earliest duelist, Toby Tredwell, was unable to withstand the procedure meant to test his abilities. Believing him to be weak and useless, Sayer ordered the intensity of the electric shocks to be amplified, which caused the young boy's death. He also does his best to keep his prized duelist Akiza secluded from anyone outside the Arcadia Movement to keep her full of hate and resentment at the world for his goals, as well as hide his own secret motives. To this end, he gasses Luna, Leo, Yanagi and Bolt Tanner when they come to him for aid against the Dark Singers. Then he threatens Leo's life in a psychic duel to test if he has powers like his twin sister Luna. Later that day he has another Psychic duel with and murders Carly Carmine by sending her through a window with a direct attack, kick-starting her rebirth into a Dark Signer. He then returns from his Disney Death at the hands of Carly, posing as a security agent to attack Yusei and Mina. Sayer states that anybody who falls prey to him will simply follow his orders and nothing more, as he takes full advantage of that individual's weaknesses.
- Lawton, meanwhile, is a tyrant lording over a small western style town called Crash Town, who forces those he's defeated to join him or face slavery in the mines. He gets into a match with Yusei while Yusei and the gang are trying to escape the mines, but before it can be decided, he throws a stick of dynamite at Yusei, Kalin, West and Nico that results in cave-in. When it explodes, Yusei and Kalin fall off the mountain, while Nico and West are unconscious on the ground. Lawton takes them back to Crash Town, renaming it Lawton Town after Barb and him double cross his brother Malcolm. Later, not satisfied with the number of workers in the mines, he and Barb begin forcing their henchmen to Duel for their survival, which is stopped by Yusei and Kalin. Once he does start to lose his 2-on-1-handicap match against Yusei and Kalin, he quits the duel and tries to run away, but not before he abandons Barb to her fate and set off explosives in the town.
- Jean-Michel Roger is the director of security in the Synchro Dimension. Originally a member of Academia, Roger betrays the academy and attempts to take over the Synchro Dimension for himself. He creates a device that allows him to brainwash the security force into mindless drones for his future attempt at overthrowing the executive council, and conducts experiments on the dangerous criminal Sergey to turn him into an even more aggressive cyborg, with intention of having him crush Jack Atlas, thereby crushing the hopes of Tops and Commons alike. When Selena duels Yugo, to ensure she wins, he repeatedly alters the track for Selena to get action cards instead of Yugo, not caring that it puts Yugo in danger of falling off the track and dying. Later on during Yuya's duel against Crow, he activates a chip he installed in Yuya's helmet, painfully electrifying Yuya to force him into a more aggressive state shrugging it off when told that Yuya could die from this. When his attempts to overthrow the council and dethrone Jack Atlas fail, he blows up the security headquarters, disables all elevators except for one he has himself and Zuzu take, leaving his other subordinates to die, and decides to take Zuzu to the fusion dimension in hopes that this will cause him to be forgiven by Academia. When Jack and Crow stop this from happening, Roger attempts to open up a wormhole to suck himself and everybody in the city in it trapping them in dimensional limbo purely out of spite, telling everybody that if they won't obey him, everything in the world should disappear. Karma hits the bastard in full force when only he ends up meeting this face. A man whose arrogance, greed, selfishness and cruelty knew no bounds, Jean-Michel Roger was one of the franchise's most relentlessly vile antagonists.
- Gishki Noelia, in the metaplot. Fuses her own daughter, Gishki Emilia, and Gusto Falco into a Humanoid Abomination (this is, incidentally, basically the same thing the infamous Shou Tucker did for his Moral Event Horizon crossing) so she could be able to fight better. If that weren't enough, she later sells out the planet to the Verz/Evilswarm because she wants to be on the winning side, resurrecting Steelswarm Hercules and the Dragons of the Ice Barrier to fight for them. There's good news, though: if Dia or Ptolemys Messier 7 didn't get her, Sophia certainly did.
- Yu-Gi-Oh! Forbidden Memories has Heishin, the Big Bad invented for the game. An Evil Chancellor and Evil Sorcerer of Ancient Egypt, as soon as he gets the ancient power of the Millennium Items, he attacks the palace with his soldiers, killing various people (including the Pharaoh and his wife) and mortally wounding Simon Muran, the Prince's tutor. When the Prince tries to escape, he threatens to kill him if he doesn't give him the Millennium Puzzle. The Prince shatters it, and is transported inside of the puzzle to the present day. When he returns, he finds that Heishin has destroyed much of Egypt and Simon Muran dies from his injuries. After defeating Heishin's top mages, he finds Teana has been kidnapped and is having her life threatened in an attempt to lure the Prince into a trap to kill him, but this is stopped by Seto, his own henchmen, who sets her free and ends up being The Starscream. Heishin obtains the Millennium Puzzle and summons the Dark God, Darknite and commands him to destroy the world and make him a god. Darknite kills him in response. Petty, selfish, and so obsessed with power that he'd try to murder underage kids in his pursuit of it, Heishin was a monstrous individual.
- Konami recycled Heishin's character in Yu-Gi-Oh! The Duelist Of The Roses, a game with a plot set during the War of the Roses, with him cast in the role of Richard III. Seeing as Richard III is famous for his Historical Villain Upgrade into a Complete Monster in Shakespeare's play, this role suits Heishin rather perfectly. Here he again shows his disregard for the lives of young people when he threatens to kill Pegasus Crawford's son.