Ash Ketchum: Stop, Kodai! All the trees and flowers will die!
Kodai: What do I care?! As long as my visionary powers grow, it's all worth it!
Ash: So you don't care what happens to Crown City?!
Kodai: It's true that twenty years ago when I touched the Time Ripple, Crown City withered, but no one knows a thing about that, just as no one will know what I've done today. All anyone knows is that I'm doing my level-best to capture the "evil" Pokémon Zoroark. (cackles evilly) VICTORY IS MINE!! (cackles even louder)
Pokémon has existed since the Game Boy era with many hundreds of Pokémon and counting being made for the goal to "Gotta Catch Them All". While most Pokémon are non-malicious, many of the worst villains prove that Humans Are the Real Monsters.
Character names are from the English dub.
Entries in each group are by original release date.
- Legends: Arceus: Volo, a seemingly perky yet dissatisfied member of the Ginkgo Merchant Guild, wishes to subdue Arceus and use its power to destroy reality in favor of his own world. To this end, Volo allies with Giratina, having it create the space-time rift, which both drives Pokémon across Hisui into dangerous frenzies and threatens to destroy the world. Manipulating the player into collecting Arceus's Plates, Volo, after revealing his true intentions and being defeated, summons Giratina to kill the player.
- XD: Gale of Darkness: Ardos, one of the sons and Co-Dragons of Cipher's leader Greevil, shows himself to be the most vicious and fanatical member within an already monstrous organization. Ardos is fully involved and supportive of Cipher's worst atrocities, involving the mass corruption of Pokémon into becoming unfeeling Shadow Pokémonwhereupon they'll be rendered unable to be purified and massed into an army through which Cipher will control the world. When Greevil is defeated, Ardos, in a last moment of desperation, attempts to cajole his father into killing the child protagonist by wiping out their base on Citadark Isle—taking all his subordinates in the building with it, to which Ardos merely scoffs "such things can be replaced". Even in the post-game, Ardos is as dedicated to the Cipher agenda as ever even when his father has surrendered himself, coldly informing the protagonist they are now Ardos's top target.
- Mystery Dungeon: Explorers: Darkrai serves as the true Big Bad. He was responsible for the collapsing of Temporal Tower that lead to the Bad Future, tortures an innocent child with violent nightmares to lure out the Player Character and their partner, and makes several attempts to assassinate them so he can try his plans again. One of his most heinous acts involves trying to have the heroes willingly commit suicide by tricking them into thinking their existence is threatening the space-time continuum due to time travel shenanigans. A Manipulative Bastard par excellence, he has no regrets for his crimes and wishes nothing more than the complete and utter destruction of the world, just so he can rule the tattered remains.
- Ranger: Guardian Signs: Purple Eyes is the nefarious leader of the Pokémon Pinchers and a true sociopath who eclipses even the Societea in cruel ambition. Kidnapping and brutalizing Rand before the plot and pulling the strings behind Red Eyes and Blue Eyes, Purple Eyes debuts in the midst of holding Rand's family hostage and torturing his young daughter Nema. After he's sold as a lost cause by Dr. Edward, Purple Eyes raids the parts of the Golden Armor from the other Societea members, usurping Dr. Edward's position and controlling Mewtwo into finishing him off—gleefully brushing off Rand's apparent sacrifice once he takes the bullet. Once he's defeated, Purple Eyes allows himself to die with the full knowledge that without the Golden Armor's power, the fortress he and the Rangers are on will plummet into the ocean and create a tsunami powerful enough to wipe out Oblivia and everyone in it. Purple Eyes truly comes into his own in the story's last extra mission; after repeated interrogation, Purple Eyes snaps and decides the only logical course of action is to exterminate all humanity and recreate it as its supreme god, attempting to goad Arceus into killing off all humans whilst leaving himself as their sole survivor.
- Diamond and Pearl:
- Cyrus, leader of Team Galactic, completely lacks the magnificence and genuinely good intentions that defined his game counterpart. Cyrus seeks to use the power of Dialga and Palkia to create a perfect new world at the knowing cost of the old one, and demonstrates a total Lack of Empathy in gathering the components for this plan, at one point ordering a the hugely-populated Iron Island destroyed simply to kill Ash Ketchum and his allies. Ultimately, after having employed the equally-ruthless Hunter J toward his cause, Cyrus tortures Dialga and Palkia into creating a "new world" for him, and he promptly attempts to abandon all of Team Galactic to die with the old world so he can experience perfection alone.
- Pokémon Hunter J is a remorseless poacher of Pokémon who hunts rare Pokémon, petrifying them and selling them on the Black Market. Hunter J has no compunction not only stealing from innocent trainers, but petrifying them as well and leaving them to die. Employed at numerous points during the season to capture innocent Pokémon—including by Cyrus—Hunter J dumps numbers of her own men off her ship without caring if they live or die; happily tortures people; and has her Salamence raze a densely-populated forest just to flush out and kill Ash.
- Zoroark: Master of Illusions: The Big Bad, Grings Kodai, is a powerful businessman who discovered one of Celebi's Time Ripples. Gaining its power at the price of annihilating the nearby city's plant life, Kodai used this power for his own greed. In the present, Kodai kidnapped a Zoroark's baby Zorua, importing the baby into another region and using blackmail to force Zoroark to terrorize innocents to make himself look good. He intended to renew his abilities by touching the Time Ripple again, at the threat of once again devastating the ecosystem solely for the money. Once Zoroark tracks Kodai down, Kodai threatens Zorua's life, electrocuting it with his gauntlet to almost fatal extents to prove he was serious. Upon being tricked by Zoroark, Kodai loses it and instead electrocutes Zoroark to death in his fury, just as the two were finally being reunited.
- Volcanion and the Mechanical Marvel: Cabinet Minister Alva is a cruel, scheming man who seeks to usurp control of the Azoth Kingdom through force. Alva devised a technique known as the Mega Wave, forcefully and painfully trapping Pokémon in their Mega Forms, using them in his attempt to take the power of Magearna. Alva assures Magearna's compliance by torturing Ash and his friends, before tearing out Magearna's mechanical heart, forcing Racel to watch. Using Magearna's heart to empower his flying fortress, Alva attacks the Nebel Plateau, forcing Magearna to ravage its own home, and spitefully tries to destroy the plateau and everything on it by letting his fortress plunge into it.
- Secrets of the Jungle: Dr. Zed is a cruel, egomaniacal scientist seeking the healing power within the Sacred Tree of the Zarude, all to glorify his own ego. With no regard to any life, human or Pokémon, but his own, Dr. Zed murdered his colleagues Chrom and Phossa Molybden by running them off the road, barely missing their infant son Al in the process and cutting the baby off from human civilization for ten years. When he learns Al survived years later, Zed tracks him to the Sacred Tree, lays waste to the forest, and attempts to desolate the entire colony of Zarude so he can rip the healing power right from its source.
- Adventures makes the following villains much, much worse than in the games and anime:
- Yellow: Agatha of the Kanto Elite Four was the brains behind the group's operations and its one truly vile member. Desiring to settle a petty grudge against Professor Samuel Oak and prove that only the truly strong trainers can spearhead the future of Pokémon, Agatha coaxed Lorelei into becoming her protégé by playing on her trauma, spurred Lance's desire to Kill All Humans, and brainwashed the honorable Bruno. Agatha was also particularly sadistic in her methods, such as nearly killing her own pawns; threatening the life of an innocent child accompanying Blue; trying to drain the life from Blue and Koga; and mentally enslaving armies of Pokémon into being living weapons for terrorist attacks on cities. Unlike her comrades, Agatha's motives are entirely self-centered, and she never plays fair in a fight.
- Black & White; Black 2 & White 2: Ghetsis Harmonia Gropius is the leader of Team Plasma, posing as a kind person seeking Pokémon freedom from trainers, but is in truth a sociopath who plans to disarm trainers and exploit Pokémon so that he can conquer Unova and from there the world. Viewing his son N only as a tool, Ghetsis raised N in an isolated environment and groomed him to be the hero of legend later, savagely beating N with his cane when N opposed him. Ghetsis also used hypnosis on several people, making them release their Pokémon companions. When battling Black, Ghetsis attempts to have the boy and all his Pokémon burned alive by flames, and then has them sealed inside the Light Stone. Ghetsis later captures Kyurem and forces it to decimate many cities, freezing populated areas solid, planning to cover the entire continent in ice. Ghetsis is willing to kill anyone who opposes him, even his own son, to the point where he self-destructs the Plasma Frigate to end his own life and the lives of everyone on board, including thousands of captive Pokémon.
- Phantom Thief Pokémon 7: Io is a ruthless Team Galactic member who won't hesitate to eliminate anyone, even her own subordinates, and treats her Pokémon as little more than weapons that she can hurt and use to hurt. Five years prior to the story, Io kidnapped Hiori's twin sister, Lily, when both kids were only 5 years old. Io conducted experiments on Lily's mind that wiped her memory of her old life and then brainwashed her into being a member of Team Galactic. When Lily gets her memory back and turns against Team Galactic, Io takes her frustration out on her henchman by having her Pokémon attack him, calling him worthless before attempting to kill both Lily and her brother. Io sought to usurp control within Team Galactic and then Take Over the World by using Darkrai's Hypnosis to enslave the minds of every living being. When warned that this could also ravage the planet and cover it in darkness, Io doesn't care so long as she can reign supreme.
- Diamond and Pearl Adventure!: Charon, while bad in Pokémon Platinum, is worse here. He introduces himself by ordering his agents to suicide bomb a crowded stadium, the explosion potentially destroying the whole town were it to spread. He holds no regard for the lives of others and plans to control the world with money made from selling legendary Pokémon, as well as to extort more money from the masses by threatening them with the power of Giratina. He also conducts nasty experiments on Pokémon that shuts off their hearts and essentially turns them into living weapons, Koya's Growlithe being among his victims, and we see him use a bunch of Skuntank under Mind Control as explosive weapons against the opposing trainers. Charon doesn't even treat his colleagues within Team Galactic well, as he captures the organization's previous leader, Cyrus, and tries to kill two of his top officers when they leave to find him. Cyrus goes on to rally the remaining agents against Charon, despite he himself previously trying to destroy the universe. Thinking only of himself the whole way through, Charon ends the series the sole character to reject The Power of Friendship as a concept and thus ends up thoroughly irredeemable.
- Arceus and the Jewel of Life manga retelling, by Makoto Mizobuchi: Marcus/Markus lacks the good intentions of his anime counterpart. Upon learning of Damos's acquiring the Jewel of Life from Arceus, Marcus decides to steal it for himself by using his Bronzong to hypnotize Damos and lure Arceus into a trap, then has all of his Pokémon electrocute him to death. Marcus uses a special armor to control the Pokémon and beats them if they rebel. When the heroes of the present travel to this era to prevent the event from taking place, Marcus improves his trap by pouring silver water onto Arceus, while his Pokémon carry out their usual commands. When the heroes learn and warn Marcus that his action will damage the space-time continuum, he admits he doesn't care and is glad to see this happen as it would make him feel like a god. When the heroes foil Marcus's plan, he kills himself, activating a mechanism that would collapse the temple and kill hundreds of Pokémon and humans out of sheer spite.
- Episodes 13 through 15 (Generation V): Ghetsis is a cruel, selfish man seeking total world domination, and the driving force behind all the evil acts of Team Plasma. In "The Uprising", Ghetsis has ordered his six chosen Sages to lead an attack on the Unova League, where they attempt to kill the young Iris and all the other Gym Leaders who oppose Team Plasma's effort to take Pokemon away from trainers by force. In "The Frozen World", in order to seize the DNA Splicers, Ghetsis has Sage Zinzolin and his forces launch a terrorist attack on Opelucid City, that's shown to endanger civilian lives and create massive collateral damage as the city gets frozen solid, leaving all in it to suffer. Finally, "The King Returns" sees Ghetsis attempting to freeze all of Unova, using the DNA Splicers to force Reshiram and a controlled Kyurem to fuse, and ordering White Kyurem to directly assault and destroy Ghetsis's own foster son N with an Ice Burn, all to remove any obstacles to his insatiable lust for power.