Manga and Second Series Anime
- The Spirit of the Millennium Ring, known as Yami Bakura, or Dark Bakura, was the longest running antagonist of the series, and one of its worst, though his actions between the manga and anime were different.
- Manga: Dark Bakura first possessed Ryo Bakura at a young age, using him to murder Shadi and attack his students. As Bakura grew up, whenever any of his friends tried to play games with him, Dark Bakura would trap their souls inside RPG figures, putting them into comas. When Yugi Mutou and his friends come over to play the Monster World RPG game that Bakura himself created, Dark Bakura traps them in figures as well over the course of the game before trying to kill them. After this, he fakes a HeelFace Turn and gets the gang to believe that he's trying to help them—although they don't trust him—and then kills Maximillian J. Pegasus and steals his Millennium Eye behind their backs. During Battle City, he stabs himself in the arm and then reverts back to normal Bakura so that Marik can gain the groups trust and then murders Ghost Kozuka after a Duel to take his Puzzle Card. In the final arc, Dark Bakura constructs the Shadow RPG to recreate Atem's final battle, including the ensuing destruction, to summon Zorc Necrophades, who will then proceed to destroy the world, again if he wins the game against Dark Yugi. He duels Katsuya Jonouchi and Yugi at two separate occasions and nearly kills them both, and in a last ditch effort destroys Atem's tomb to kill the group.
- Anime: The Spirit of the Ring was possessing hero Yugi's friend Bakura Ryou for almost the entire duration of the series. During the Duelist Kingdom arc, he traps Yugi Muto and his friends within the card game, resulting in them being sent the graveyard if defeated. He subsequently tries to kidnap Mokuba Kaiba, and rips Maximillian Pegasus's Millennium Eye out of his eye socket, leaving him in a coma. During Battle City, he infiltrates the tournament and kills Bonz, Zygor, and Sid before trying to do the same to Yugi and Yami. Failing, 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 Seto Kaiba into a Shadow Game, then traps Yami in the Memory World, possessing his own past self, Thief King Bakura, in the process. Eventually possessing Tristan Taylor as well and pulling a You Have Outlived Your Usefulness on his own past self, The Spirit of the Ring unleashes Zorc in the past, while taking on Yami in his final Shadow Game in the present, with the intent of unleashing the apocalypse upon the world.
- Dark Marik, or Yami Marik, is the twisted Split Personality who drove the real Marik Ishtar off the deep end in the first place. Seizing control of Marik's body during his childhood, he killed their abusive father, and 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 kill Yugi; these included kidnapping; Mind Rape; brainwashing; and attempted murder. Unleashed in the Battle City Finals, Dark Marik horrifically and painfully tortures any duelist he comes across, trapping Mai Kujaku/Mai Valentine in her own mind to die horribly; making Bakura vanish; and leaving Jonouchi/Joey Wheeler comatose, all the while making attempts on his siblings' lives. In his final duel, Dark Marik puts up Yugi's soul and his normal personality as sacrifices in an attempt to either kill Yugi once and for all or rid himself of any chance of being suppressed again.
- The Great Evil God Zorc Necrophades/Zorc the Dark One is a primordial demon fueled by darkness, influencing humanity's corrupt actions for his own amusement. Making contact with Priest Akhenaden, Zorc used him to create the Millennium Items, resulting in the town of Kul Elna being slaughtered except for a child. Summoned into the physical realm by Akhenaden years later, Zorc rampaged against the armies of Pharaoh Atem, killing many and forcing Atem to seal himself and Zorc inside the Millennium Puzzle. Acting through proxies 3000 years later, Zorc's battle with Atem is recreated in the Shadow RPG, with the demon intending to win and resurrect in the real world. Zorc's ultimate goal is to destroy the world and replace it with an "endless hell" of darkness and suffering.
- The original version of the Light of Destruction stands out as one of the most heinous villains in the franchise. A celestial entity that finds bliss in destruction, the being is revealed to be the true Big Bad of the second season. Prior to the story, the entity corrupted the pro duelist, DD, into murdering the father of Edo Phoenix for the card, Destiny HERO-Plasma. The Light of Destruction then had DD trap his soul inside the monster, before delivering the same fate to countless duelists. When possessing the fortune teller, Takuma Saio, the Light of Destruction gains access to the dangerous satellite, SORA, intending to use its laser to wipe out all life on Earth. After defeating Edo, the Light places him on top of a high scale, telling Judai that he'll fall to his death unless he gives the entity the remaining key to activate the satellite. When Judai complies, he attempts to have Edo fall anyway. During his duel with Judai, the Light of Destruction states that the universe is destined to be led to destruction, and that he intends to create a cycle of constant re-creation and destruction of the universe. He then attempts to mentally torture Judai in the hope that it breaks the latter's spirit.
- Season 3: Brron, Mad King of Dark World, is demented and sadistic, ruling the Spirit World as its vile dictator and being responsible for its deplorable state and the 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, before dying, spitefully mocked Jaden by saying that he would never see his friends again.
- Divine, known as Sayer in the dub, 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 Lola/Toby Tredwell, was unable to withstand the procedure meant to test his abilities. Believing him to be weak and useless, Divine ordered the intensity of the electric shocks to be amplified, causing the young boy's death. He also does his best to keep his prized Duelist Aki Izayoi secluded from anyone outside the Arcadia Movement to keep her full of hate and resentment at the world for his goals, as well as to hide his own secret motives. To this end, he gasses Luca, Lua, Yanagi and Jin Himuro when they come to him for aid against the Dark Singers. Then he threatens Lua's life in a Psychic Duel to test if he has powers like his twin sister Luca. Later that day he has another Psychic Duel with and murders Carly Nagisa by sending her through a window with a direct attack, beginning 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 Mikage Sagiri. Divine 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 weakness, just like he did with Aki.
- Lotten, known as Lawton in the dub, is a tyrant lording over a small western style town called Crash Town, where he 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, Kyosuke Kiryu, West and Nico that results in a cave-in; Yusei and Kiryu fall off the mountain, while Nico and West are unconscious on the ground. Lotten takes them back to Crash Town, renaming it Lotten Town after Barbara and he double-cross his brother Malcolm. Later, not satisfied with the number of workers in the mines, he and Barbara begin forcing their henchmen to Duel for their survival, which is stopped by Yusei and Kiryu. Once he does start to lose his 2-on-1-handicap match against Yusei and Kiryu, he quits the Duel and tries to run away, but not before he abandons Barbara to her fate and sets off explosives in the town.
Arc V anime
- Jean-Michel Roger/Roget, the Arc Villain of the Synchro Arc, is the director of Security for 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 Yuzu take, leaving his other subordinates to die, and decides to take Yuzu 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.
- Forbidden Memories: Heishin is 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 has died 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, Heishin's own henchman, 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, to which Darknite responds by killing Heishin. Petty, selfish, and so obsessed with power that he'd attempt to murder teenagers in his pursuit of it, Heishin was a monstrous individual.
- The Falsebound Kingdom: Scott Irvine traps Yugi, his friends, and the Kaiba brothers in a multiplayer RTS game in an attempt to feed their souls to DarkNite, a wicked spirit, who will then Take Over the World. When the virtual villain Emperor Haysheen is defeated, Scott deletes him from the game and assumes his position, brainwashing Yugi's friends into attacking him or attempting to kill everyone in the game; if the player fails to free Tea or Joey, everyone is destroyed or Scott forces Joey to kill himself, gloating all the while. He additionally steals Mokuba's soul to blackmail Kaiba into fighting Yugi, adding that he'd kill the young Mokuba if Seto doesn't do as he says. When the heroes finally reach him, Scott reveals his plan and attempts to tribute their souls, and succeeds in killing everyone should the player fail. He also deletes other sapient NPCs from the game, and a prequel campaign reveals he was toying with an NPC version of Marik by manipulating him and making false promises of power. Cruel, merciless, and arrogant, Scott does everything in his power to achieve his goals and cares nothing for anything else.
- Master Guide 6: Lee is the main villain of the World Legacy story. Originally a scientist studying the World Key, an artifact of unimaginable power, she decided to use it to awaken the power at the planet's core, which would allow her to become a god. The act nearly destroyed the world, and wiped out most life on it. Though she was killed in the aftermath, she bound her soul to the created World Chalice. Much later, Lee came across 3 heroes, Ib, Ningirsu, and Auram, and their pet dragon, and convinced them to gather the World Legacy artifacts that were created as a part of the World Key's activation. At first seeming benevolent, she reveals her true colors in front of Ib, and takes control of her body. Though defeated when Ib regained control, Ib was forced to kill herself in the process. When Ningirsu tried to revive Ib, it was revealed that Lee survived in the robot Ningirsu created for Ib's soul. Lee then seemingly destroyed Ib's soul, all while attempting to become a god once again, not caring about the world being destroyed.