Magnificent Bastard/Pokémon

The most magnificent masterminds of the Pokémon franchise are listed here: 

"Never forget that all Pokemon exist for the glory of Team Rocket!"

Core Games

• Pictured above: Team Rocket's boss Giovanni is the quintessential villain in the franchise. He has been portrayed as this trope in adaptations, and his gameverse incarnation eventually attained this status when he resurfaced as the leader of Team Rainbow Rocket in Ultra Sun and Ultra Moon, pulling alternate universe versions of other team leaders to help him. Taking advantage of the Ultra Wormholes, Giovanni invaded Aether Paradise, taking Aether Foundation president Lusamine hostage. Giovanni planned on using their technology and research to gain an army of Ultra Beasts, and even when defeated, simply pulled out while setting his sites on another world. Further appearances in Let's Go! Pikachu and Eevee Versions, Pokemon Go!, and Pokemon Masters have only continued to show how diabolical and ruthless yet still fair playing Giovanni is and how he's often working many schemes for global domination seemingly at once, with the notion of his schemes being challenged and opposed by strong young trainers doing nothing to deter him from his ambitions - in fact, the prospect only ever excites him, for he values strength and respects those who showcase it. Although cruel, Giovanni is also honorable and polite, and is willing to yield if he and his team benefit in the long run.
• The core game series also has Cyrus, Big Bad of the Generation IV games and boss of Team Galactic. He's shown to always be steps ahead of you or the other good guy characters, has an intricate criminal/terrorist operation carried out while using his team doing official business for his energy company as a front for these crimes, is highly intelligent and calculating, and has enough charisma to sway the spirits of his followers and deceive them into following his stated cause of using the powers of time/space to Take Over the World and change it for the better, when in reality he plans to literally destroy the existing world with these powers and create a new one where all living things would be stripped of spirit (what he believes is the source of all strife and incompleteness in the world) and he'd reign over it as God of a new universe. As a master of suppressing his emotions, he rarely ever loses composure and is strangely respectful and courteous towards his enemies too. Unlike other villains, he claims to not use Pokemon as friends or tools, but instead make their power his own through his man-made devices fueled by their energy such as the Red Chain. Cyrus ends up being so magnificent that even his enemies revere him. Although suffering a Villainous Breakdown, Cyrus quickly regained composure, vowing to never give up on his dream. A very ambitious man, Cyrus's polite and philosophical exterior offset what was a horrible vision he had for the world.
• Colress was the acting leader of Team Plasma in Black 2 and White 2, and unlike Ghetsis, he plays this trope straight. A scientist looking for the best way to bring out a Pokémon's strength, Colress traveled across Unova and battled trainers to craft a theory for him to test out. As part of Team Plasma, Colress invented a machine to maximize the full extent of Kyurem's power and fire it upon the world, freezing Opelucid City in the process. Admitting that he doesn't care about his cruel actions, Colress engaged the protagonist in battle to test out his theory on hidden potential and upon defeat allowed them to face off against Ghetsis to develop his theories more. Showing no loyalty to Team Plasma or Ghetsis, Colress is such a seemingly nice person that it is easy to forget that he never regretted almost destroying Unova.
• Black 2 and White 2 Poke' Star Studio films:
  • Brycen-Man series: Brycen-Man is an ambitious and hammy supervillain who seeks to Take Over the World. After his first defeat to the Riolu Kid, Brycen-Man attacks a pier as a front to steal a powerful black diamond from within an ocean liner. Though the Lucario Kid stalls him and the liner departs, Brycen-Man manages to steal the diamond anyway by swimming after the liner, using it to build his Brycen Jet and give himself tremendous power. In the final showdown against the Lucario Kid, Brycen-Man is weakened due to the diamond's effects and accepts his end, but the Kid's genuine admiration for him convinces him to declare them his archrival.
  • Invaders series: E is an alien whose home planet was destroyed by a supernova, leaving the remaining members of her species homeless. Seeking to destroy all life on Earth so her people can inhabit it, E leads UFOs into the Unova region to attack people and Pokémon. Disguising as a human, E convinces the player, a member of the Unova Defense Force, to help set up a decoy UFO to lead the aliens' mothership to Earth and humanity to extermination. E is eventually forced to leave when the mothership sees Earth as dangerous, but keeps the player’s proposal for the two species to coexist in mind. In the worst endings of the final movie, E instead takes advantage of the player's emotions and turns them into her servant to assist the aliens in world conquest.
• The Big Bad of Generation VII, Lusamine, may be among the most successful and manipulative villains in the core series. While in Sun and Moon she's held back from attaining full magnificence by toxin-induced mania that drives her into wild emotional mood swings and acting impulsively and irrationally, she's a straightforward example in Ultra Sun and Ultra Moon, where she's not mentally impaired in any way, with all of her actions being done entirely of her own will. In this version, as in the original Sun and Moon, Lusamine runs the Aether Foundation and earns trust and support by putting on the image of being a loving and caring person even while secretly freezing dozens of rescued Pokémon that she liked the best in order to keep them preserved in her hidden chamber like decorations, manipulating Guzma and the rest of Team Skull into doing her bidding (meaning that she controls two different organizations at once), and controlling the lives of her children, Lillie and Gladion, to an extent where they're powerless to stop her once her plan starts coming together. Finally capturing Cosmog when she has Lillie abducted, here she does it all for the ends of opening a single Ultra Wormhole so that she can capture/defeat Necrozma in Ultra Space and save Alola's light, and she takes advantage of the Ultra Recon Squad by making them believe that she's going to use a different means to stop Necrozma when she actually intends on dealing with the beast all by herself for her own personal, more self-centered reasons. Even when she loses a battle to the Player Character, thus failing to prove that she has the strength to handle Necrozma and Ultra Beasts on her own, she says that since she has Guzma with her, she's not on her own before using Cosmog to open the Wormhole to Ultra Space anyway. Her only failure was overestimating her and Guzma's ability to neutralize Necrozma as a threat once it starts flying into a rage. After being talked down by Lillie and made to see the error of her ways, Lusamine accepts her failure with grace and relinquishes the hold she had on her kids, resuming duties as the Aether Foundation's leader and focusing on turning herself and her company's work around for the better. In spite of her many personal failings, Lusamine in these games inspired such respect with her charm, intelligence, and the strength of her will that Lillie and Guzma don't hesitate for a second to go and rescue her from Giovanni and liberate Aether Paradise from his Team Rainbow Rocket in the post-game.
• Pokémon Legends: Arceus:
  • Cyllene, Captain of the Galaxy Team's Survey Corps, is the distant ancestor of Team Galactic's Cyrus in the feudal-era Hisui region who is responsible for the study of wild Pokémon. Upon meeting the player, she tests them by sending them out on a dangerous mission to collect wild Pokémon, with the threat of banishment from Jubilife Village (and death in the wilderness) in the event of failure. Once the player passes, Cyllene regularly sends them out to further research the wild Pokémon. When Commander Kamado banishes the player, Cyllene discreetly aids them against his orders and eventually reinstates them into the Galaxy Team. While outwardly cold and analytical, Cyllene showcases the ability to care for others on multiple occasions, and will put what she believes to be the greater good first ahead of even her position.
  • Volo, despite being downright evil, shows traits of magnificence as well. Being part of the Ginkgo Guild, he initially seems like a friendly and helpful guide to the Player Character by guiding them in their quest and helping them when they are in need. However, he is later on revealed to be a researcher and devout cult-like follower of Arceus with a god complex who works with Giratina in order to destroy and recreate the world. Aside from very vague hints here and there, Volo never said or did anything to suggest that he was a straight up villain before his true self is revealed, but The Reveal perfectly aligns with his actions and previous interactions with the Player Character, which the player might only realize too late. Like Cyrus, he even manages to recover from his Villainous Breakdown surprisingly quickly, showing that even when he gets frustrated, he doesn't completely lose his composure and he even accepts the fact he lost in the end while still vowing to realize his vision for the future in some way before walking away unpunished for his actions.
• Pokémon Scarlet & Violet:
  • The Final Boss(es) of the main game may caught many players off-guard for how truly twisted yet ingenious they are: Professor Sada (in Scarlet) / Professor Turo (in Violet) was Arven's parent who discovered and utilized the Terastal phenomenon while exploring the Great Crater of Paldea. The Professor proceeded to use the Tera crystals to create a time machine with hopes of building a paradise for their family, using the machine to bring over Pokémon from the past/future, in spite of their threats to Paldea's ecosystem. Even with the Professor's untimely death as a result of their research, their numerous security systems and failsafes, including forcing their AI copy to battle any threat to the machine and, in the event that would fail, locking all Poké Balls except their own, would defend the time machine from the protagonist and their friends, demonstrating the Professor's willingness to allow the destruction of the region for the creation of paradise.
  • The Hidden Treasures of Area Zero DLC: Pecharunt is the catalyst for the events of The Teal Mask and the primary antagonist of the Mochi Mayhem epilogue. A small Mythical Pokémon that was cared for by an old couple, Pecharunt loved them back but desired more of their affection. It fed them Binding Mochi made from the poison in its body which put them under its thrall and brought out their greed. It enthralled another Pokémon with its mochi named Okidogi to help carry out the couple's new wishes. The couple's love for Pecharunt grew and grew, though they were unaware that it was the reason why they now had desires for physical items. Eventually the couple asked Pecharunt to retrieve four masks created by a man from Kitikami for his companion Ogerpon. On the journey to Kitikami, Pecharunt enthralled two more Pokémon to be its retainers and use their powers to keep it safe. Using the Loyal Three's abilities, Pecharunt found the cave where the man and Ogerpon lived, and had the masks stolen. However, the man returned and a fight ensued, causing Ogerpon to defeat the Loyal Three in revenge. Pecharunt escaped into its shell and wouldn't emerge until much later. In the present day, Pecharunt manages to both trick many of the citizens of Kitikami into eating its mochi as well as simply throw it into their mouths. It is able to turn much of the region into its puppets, and have them use their Pokémon to fight for it. It even is able to take command of the player's friends Penny and Arven along with the Champion trainer Nemona, and proves itself willing to fight the player alone as well.

Side Games

• In Pokemon XD: Gale Of Darkness, Greevil was the Grand Master of Cipher, ruling the organization with his sons. Under the guise of Mr. Verich, Greevil interacted with the citizens of Gateon Port and gave free food and drink at The Krabby Club. After the defeat of the organization in Orre five years prior, Greevil restored the organization with the creation of a Shadow Lugia that could not be purified. Using the Lugia for evil purposes, Greevil worked to hide Cipher's efforts in creating an army of Shadow Pokémon, only acting when the plan was in jeopardy, such as kidnapping Professor Krane when he was inventing a purification machine or attacking ONBS when they had evidence of Cipher's return. Even when production of the Shadow Pokémon fell apart, Greevil was able to kick start the last part of the plan anyway in which Lugia would lead the Shadow Pokémon to take over the world. Upon the defeat of both him and Lugia, Greevil briefly considered destroying his base to make a getaway in spite of the loss of life before surrendering so that he wouldn't have to live with the moral consequences.
• In Pokemon Conquest, Oda Nobunaga is the Warlord of the kingdom of Dragnor and a master of Dragon-type Pokemon. Seeing his homeland of Ransei ravaged by wars to unite the seventeen kingdoms and summon Arceus before the victor, Nobunaga decides to conquer Ransei himself and destroy Arceus so these destructive wars will cease. Though the Player Character pushes back his campaign, Nobunaga feigns defeat so that they will be the conqueror of Ransei instead and summon Arceus in his place; Nobunaga then launches a surprise attack against it with his five lieutenants and an even more powerful partner Pokemon than before. He treats friend and foe alike with respect even as he confidently tells them he will defeat them, and then takes his loss with dignity and acknowledges his opponent's power if they prevail. Nobunaga's reputation as the greatest Warlord in all of Ransei is well-earned.
• Pokepark 2: Wonders Beyond: Darkrai plots to turn his dimension into a land where all Pokémon can have fun forever. Turing it into Wish Park, he hires multiple Pokémon and has them either advertise the park or kidnap unsuspecting Pokémon, where he then hypnotizes them using the attractions, acquiring half of each area's Pokémon by the events of the game. Having his men hinder Pikachu and his pals, he eventually takes action himself and mind-wipes his friends into forgetting about Pikachu, briefly leaving him alone and lost. Truly believing in his cause, when Darkrai learns of his unintentional creation of the Dark Vortex, he abandons his scheme to help stop it, Even performing a Heroic Sacrifice to shut it down. Rescued by a grateful Pikachu and Pals, Darkrai vows to change his ways, turning Wish Park into a real theme park.
• Pokemon Mystery Dungeon Explorers
  • Dusknoir is Primal Dialga's right-hand man who pursues the player and Grovyle into the past. He poses as a friendly explorer while using his knowledge of the future in order to pick up information. He successfully deceives Treasure Town into helping him capture Grovyle, thereby dooming the future to paralysis, and even drags the amnesic player back to the future as a precaution. Once Grovyle, the player, and their partner escape, Dusknoir allows them to find Celebi, intending to capture her once she reveals herself. He brings along Primal Dialga to accompany him and the party is barely able to escape him. Despite his ruined reputation, he lies in wait in the past and forces Grovyle to sacrifice himself by dragging them both back to the future. Once they arrive in the future, he earns Grovyle's trust and lures him into a trap in an attempt to hijack his body. If it wasn't for the conscience he'd developed convincing him otherwise; Dusknoir's plan would gone off flawlessly
  • Darkrai is the true mastermind behind the destruction of Temporal Tower, which he sabotaged so he could create a world of darkness to rule. When Grovyle and the player traveled back in time to stop it, Darkrai attacked them within the Passage of Time. This separated the two, as well as giving the player amnesia and transforming them into a Pokémon. After Temporal Tower is saved, Darkrai decided to distort space in order to create a world of eternal nightmares. Disguising himself as Cresselia, Darkrai blamed the player and their partner for the distortions, and convinced Palkia that their deaths would restore everything back to normal. Once his ruse was revealed, he retreats to Dark Crater and puts the player in an illusion to convince them to join him. When that fails, he reveals an army of six other Pokémon to help him kill the player. As a final back-up plan, he has a dimensional hole ready for a quick getaway, only being stopped by the timely arrival of Palkia.

Anime

• Giovanni, boss of Team Rocket, has always been this trope in the anime. He approves of plans that he finds clever and supports agents that give him the best results. At the same time, Giovanni allows his less competent agents to do what they want if they don't get in his way. After the incident with Mewtwo, Giovanni tracked it down and captured the clone Pokémon to use as hostages before trying to force Mewtwo to obey his will. Discovering the Meteonite in the Unova region, Giovanni planned to use its power to coax business leaders and politicians into giving him power. Later on, Giovanni led the operation to capture Meloetta and use its power to control Tornadus, Thundurus, and Landorus. Possessing both cruelty and mercy, Giovanni has never let go of his ambitions for world conquest.
• In the Original Series episode "The Ghost of Maiden's Peak", a talking Gastly masquerades as the ghost of a legendary maiden for the annual Summer Festival at Maiden's Peak. Gastly uses his wits and the maiden's form to lure in Brock and James and drain them of their vitality, having done the same to many men at past festivals. Along the way, Gastly also turns into an old lady to "warn" the travelers and scam them with cheap ofuda. When the protagonists expose him, Gastly uses illusions to exploit each of the Pokémon's natural weaknesses. Though the morning sun dispels him, Gastly ends up thanked by the maiden's actual ghost for keeping her legend alive.
• From the Ruby and Sapphire series: Brodie, the Man of a Thousand Faces, is a thief initially under Team Magma's employ. Disguising himself as a scientist named Millie, Brodie stole data on Groudon and Kyogre from the Weather Institute, successfully fending off Team Aqua in the process. After Team Magma's dissolution, Brodie became a lone thief, stealthily nabbing the Ribbon Cup while it was being transported to the Hoenn Grand Festival. Evading attempts at capturing him, Brodie eventually surrendered the trophy willingly before escaping justice.
• In the Diamond and Pearl series episode "Where No Togepi Has Gone Before", the evil Togepi seeks to amuse herself at the expense of others. Wandering into Team Rocket's newest base, Togepi steals their food and causes torment for both the trio and Ash and his friends while simultaneously creating the role of a "good Togepi" to trick everyone. After being found out, Togepi used Attract to control their Pokémon and hijack Team Rocket's space ship, with the intention of going "to the end of the universe". Only stopped by the combined efforts of Happiny and Rayquaza, Togepi used Psychic to save everyone before leaving to rest and cause strife elsewhere.
• Best Wishes series:
  • Team Rocket's Meowth, of all people, attempts to be this at one point in this series. During the journey to Nimbasa City, he played the gang like a fiddle by pretending to be fired from Team Rocket and wanting to join with them instead, and nearly got away with their Pokemon along with the other members of Team Rocket (Jessie, James, and Dr. Zager), who were all operating a surprisingly well thought out plan. Unfortunately for them, it's another situation where Failure Is the Only Option.
  • Dr. Colress, acting leader of Team Plasma in the "Episode N" arc of Best Wishes, matches Meowth in charm and efficiently quick thinking as he was able to play off of his overconfidence to dupe him into becoming his test subject to use against Team Rocket. Unlike the rest of Team Plasma who seek to control Pokemon for World Domination, Colress is in it purely For Science!, having no true respect for Team Plasma's leader Ghetsis (he does not speak to him with the same reverence as his grunts do), constantly thinking well ahead of anyone else he may be sharing space with, and always advancing his technology so that he could better control the minds and hearts of Pokemon in order to strengthen them beyond their limits, even Legendaries like Reshiram. And he did all this in his own style with a perky, exuberant attitude towards his work, not minding at all that he was taking an amoral approach to bring out the full strength of Pokemon because he justified it as being in the Pokemons' best interest as well. Even in the end, the guy doesn't let crushing failure and getting arrested get him down: he just vows to move on to a new approach: finding a way to communicate with Pokémon directly!
• Lysandre from the XY&Z series is no slouch either. The CEO of Lysandre Labs and secret leader of Team Flare, he tricks Alain into retrieving Mega Evolution Energy and an ancient stone he needs for his plans to revitalize the Kalos region, roping along Hoenn Champion Steven Stone while doing it to battle some out of control Legendary Pokémon, and for most of his tenure in the main series he's a Villain with Good Publicity of the highest order. By the time he finally executes his scheme, not only is everyone caught by complete surprise, but when an organized resistance composed of Ash's group, Alain, the Kalos Gym leaders, one of his own followers, and not one but two Champions oppose him, he turns out to be Crazy Prepared and has several solid contingencies in place. He didn't see Zygarde having another transformation coming, though.
• Pokémon Generations: Giovanni is the leader of Team Rocket, and secretly the Gym Leader of Viridian City. Using the Celadon Game Corner as a front for Team Rocket's illegal Pokémon trade, Giovanni earned the respect of his men to the point where no one was willing to betray him. After a failed attack at Silph Co., Giovanni's actions attracted the attention of Looker from the International Police. Despite tracking him down at the Viridian Gym, Giovanni managed to elude Looker and his men in the time it took for him to give out his final Gym Badge. Taking personal responsibility for Team Rocket's setbacks, Giovanni went into hiding hoping to rebuild his criminal empire to be stronger than ever before. In spite of Looker's efforts, Giovanni managed to remain at large three years after his disappearance and still commanded the respect from the team he once led.

Movies

• Let's not forget Mewtwo's original persona from Pokémon: The First Movie. Cloned from the Mythical Pokémon Mew and enraged at his seemingly pointless existence, Mewtwo vowed revenge against humanity. Constructing the Pokémon Palace on New Island, Mewtwo brainwashed a Nurse Joy to issue invitations to the palace proclaiming to be the World's Greatest Trainer. Mewtwo then created a hurricane around the island to weed out only the strongest and bravest trainers. With those that he wanted at the island, Mewtwo battled them with his own clone Pokémon and stole their Pokémon with special Poké Balls so that he may clone them too. Intent on purging the world of all naturally born life via psychic storms and taking over the world (or just mass producing a whole race of Clone Pokémon to prove their superiority to naturally born Pokémon in the original version) in an outrageously audacious fashion, Mewtwo sets his army of clones in battle against the originals as he gets to fight Mew, from whom he was cloned. As the battle ended with Ash petrified, Mewtwo watched in amazement as both clones and original shed tears for the human, and left with the clones to find a place for them to belong while erasing the memories of everyone involved.
• Lawrence III in Pokémon The Movie 2000: The Power of One wishes to obtain the Legendary Pokémon Lugia and add it to his collection. Using the prophecy of Shamouti Island as a guide, Lawrence III attacks and captures Moltres and Zapdos, causing enough of a disturbance for Lugia to be summoned. When Ash, his friends, and Team Rocket are accidentally captured, Lawrence III releases them so they can view his collection. Even when his Cool Airship crashes, Lawrence III is still able to almost capture a distracted Lugia, and accepts the subsequent destruction of his collection, salavaging the ancient Mew card that had started it all and planning on starting over from scratch.
• Pokémon 3: Spell of the Unown: Entei, an illusionary guardian created by the Unown, makes it his personal mission to ensure young Molly's happiness as her surrogate father. Working with the Unown's power to create Molly her own kingdom, Entei hypnotizes and kidnaps Delia Ketchum to serve as Molly's mother, and encourages Molly to live out her dreams as a Pokémon trainer by dueling Ash and his friends when they arrive to rescue Delia. Though nearly defeating even Ash's powerful Charizard, Entei stands down at Molly's request, accepting the girl's maturation and desire to end the conflict before Entei sacrifices himself to take down the out of control Unown to save not only Molly, but Ash and his gang as well.
• Pokémon Heroes: Annie and Oakley are a teenage duo of notorious and highly competent thieves who travel to the waterside city of Alto Mare (assigned there by Giovanni in the English dub) in order to steal the Soul Dew and use it to activate the Defense Mechanism of Alto Mare (DMA). Once there, the greedy and thrill-seeking girls send Surveillance Drones all over town and come upon the legendary Eon Pokémon Latios and Latias. Trailing Latias through the canals, Annie and Oakley locate the Secret Garden and are able to stratetgically counter Latios and Latias' every move with their own Pokémons' techniques and their high-tech capture devices, and while Latias escapes, the thieves manage to capture Latios and obtain the Soul Dew. Finding the DMA, Oakley quickly learns how to use it adeptly and in that time she creates floods through the town, takes out the electrical grid, resurrects the evil Kabutops and Aerodactyl fossils, and even nearly drowns Ash when he tries to come to Latios' rescue. While Oakley's efficicency with the machine comes at the cost of her mental clarity, Annie, worried for her dear partner and abiding by her own standards, attempts to free her from the machine's grip. Last seen in a heavily guarded prison, Annie and Oakley are scheming a breakout so that they can steal the possessions of Lawrence III. Possessing charisma, cunning, tech-savvy, and ruthless determination on top of their impressive super-athletic abilities, grace, and style, Annie and Oakley stood as two of the coolest and most memorable antagonists in the anime.
• In Jirachi Wishmaker, Butler was on the surface a friendly magician. But unbeknownst to most, Butler was a former Team Magma scientist who vowed revenge after an experiment to create a Groudon failed and resulted in his firing. Working with his girlfriend Diane, Butler found Jirachi hibernating in a crystal and gave it to Max in order to awaken it. Capturing the Pokémon Absol to prevent it from interfering, Butler attempted to use Jirachi's true eye as power source for creating a Groudon. When Ash and friends the group escaped with Jirachi, with the help of Diane and Absol, Butler followed them with a tracking device. Ambushing them, Butler successfully used Jirachi's third eye to create Groudon. When the Groudon came out as a energy stealing monster, Butler came up with the plan to destroy it, hoping to undo all problems that he caused.
• Destiny Deoxys: "Purple" Deoxys arrives on Earth to search for its "Green" counterpart, willing to go to any lengths to reunite with its partner. Quickly reacting to the presence of Rayquaza, Deoyxs cleverly uses its various shapeshifting forms to fight off its foe, facing even total disintegration by slipping away and slowly regenerating. Years later, Deoxys invades LaRousse City, shorting out its technology and using an army of clones of itself to kidnap most of the populace, making its search for its still-missing partner easier. Anticipating the arrival of Rayquaza, Deoxys finally locates its Green counterpart, and chooses to work with Rayquaza in saving Ash and his friends from LaRousse's rogue robot army, Deoxys earning Rayquaza's respect before departing Earth for good.
• Pokémon Origins: Giovanni, the boss of Team Rocket, is once again depicted as this trope. He put together an efficient operation to have Team Rocket completely take over Saffron City, and when Red intrudes on his attempt to extort the Master Ball's secrets from the President of Silph co., Giovanni personally faces him and his Pokémon team in what ends up being a Curb Stomp Battle in Giovanni's favor. Giovanni escapes the Silph building with extorted data, telling Red that he views Pokémon to be best utilized as tools for business. Red later ends up facing Giovanni at the Viridian City Gym, of which Giovanni is Gym Leader, as the Rocket Boss puts it all on the line in order to prove his jaded, profit and power-based ideology superior to Red's idealism and friendship with his Pokémon team. Putting Red on the robes with a combination of calculated strategy and vicious brute force, Giovanni's passion for training and battling with Pokémon is reawakened in the toughest battle he's fought in ages, and when Red emerges the victor, Giovanni takes his defeat with a diginified grace, not only praising Red's skills and giving him the Earth Badge, but personally ordering for Team Rocket to be disbanded. As Red departs, Giovanni mulls over making a new start, together with his Pokémon.

Manga

• Pokémon Special:
  • Giovanni, boss of Team Rocket, manipulated nearly every event in the first Chapter of the manga via a huge criminal operation carried out under the guise of a string of seemingly unrelated incidents, had many plans (Mewtwo, the Legendary birds, the raid of Silph Co.) running simultaneously and even being altered to accommodate circumstances, and is shown to be so skilled at Pokemon battle that he can anticipate what his opponents' Pokemon will be, what move they'll make, what counterattack to use, AND how many seconds or minutes it all will take, all before anything's even happened yet, all with a suaveness, dignity, and imposing demeanor of a Diabolical Mastermind Yakuza boss. Subsequent appearances reinforce how magnificent a bastard, and what a surprisingly good sport, he is. Given he's been a trainer for YEARS, and wrote THE BOOK on Ground types & his Viridian powers, though his have not been explained, it makes sense. It also makes him a poster-boy (man?) for this trope here in this manga more than ever when compared to even the games and the anime.
  • Green also demonstrates aspects of this, despite being a heroine, particularly in the Red/Blue/Green Chapter and the Yellow Chapter, where she can best be called a Junior version of Fujiko Mine. A wayward thief and a con artist when Red first meets her, Green scams him out of his money by selling him an assortment of items that don't work properly, playing to his good nature in order to do so, and when he chases her down to retrieve his money and she finds emotionally manipulating him a second time doesn't work, she feigns falling unconscious to keep Red from noticing her swiping his two Gym Badges through sleight-of-hand. Using the badges to strengthen her own Pokemon, Green goes on to make fools of Team Rocket by stealing an important disc about Mew from them and constantly giving them the slip through clever trickery, even getting Red to help her out. Afterwards she seems to return his badges to him while she goes off to sell photographic evidence of Mew she got to tabloids...only for it to later be revealed that the badges she "returned" were fakes and she's still been holding onto the real ones for future use. During the battle at Silph Co., Green employs underhanded tactics to blindside Team Rocket's Sabrina and goads both Red and Blue into doing most of the heavy lifting for her so that she might claim the greatest prize in the end. Her strong showing at the Indigo Plateau Tournament gets Professor Oak to allow her the official runner-up status after he drops out. She then engineers nearly every event in the Yellow Chapter by setting Yellow on her quest and telling her never to remove her hat, which she bugs with a GPS beacon and recording device ("I've been... um... using Yellow as my learning aid!"), and also keeps Yellow wearing the hat so that Red remains under the impression that Yellow is a boy just for her own amusement to see how long it takes before he finds out the truth. When going up against Lorelei of the Elite Four, Green bests her through pulling a Batman Gambit where she fakes having her arm severed when in actuality the arm and the jacket she'd been wearing was her Ditto having changed form to fake Lorelei out and conceal Green's trump card. Even the Gold/Silver/Crystal Chapter has her showing an epic case of Crazy Prepared when she reveals that she conquered her phobia of Bird Pokemon by capturing the three Legendary Birds, which she gleefully turns against her corrupted pseudo-siblings, Will and Karen. While she develops into a more straight-up Guile Heroine as she matures, the sneaky, mischievous qualities that made Green such a cunning and formidable opponent never really leave her.
  • Lance in the Yellow Chapter is the leader of Kanto's Elite Four, a group of Pokemon League officials, who wishes to wipe out most of humanity and create a utopia for Pokemon by summoning the spirit of Lugia. Despite his hatred for humanity, Lance minimizes casualties as much as he can, allowing humans to live longer lives before wiping them out. After seeing how capable of a trainer Red is during the Pokemon League, he has Bruno test his abilities before having Agatha and Lorelei ambush him during the battle, resulting in Red's near death. Later, Lance and Agatha send their forces to terrorize the region, tricking their enemies into thinking they're unprepared for an attack on Cerise Island, and hides his Gyarados and Dragonite underground to ambush Blaine and Yellow during his battle with them. Even when seemingly defeated by the untimely appearance of Giovanni, Lance even manages to Out-Gambit him by tricking into coming to the center of Cerise Island, resulting in Lance successfully summoning Lugia and nearly wiping out mankind. Despite his cruel nature, Lance truly cared about making the world a better place for Pokemon, and after changing his ways following Yellow's defeat of him, works to protect humans and Pokemon alike from future threats.
  • The Masked Man/Mask Of Ice real name Pryce, Gym Leader of Mahogany Town, is the Big Bad of the Gold, Silver, and Crystal Chapter. A malevolent and eerie yet well spoken figure always hiding his face behind a mask, he controlled the Legendary Pokemon Ho-Oh to abduct six children that he took in as his own and raised to be criminals, and while the youngest of these (Green and Silver) managed to escape him and become regular, if not still thieving, trainers, the Masked Man used the other four to gain influence within Team Rocket and the Pokemon League respectively without anyone realizing it. Brainwashing remnant members of Team Rocket with Mind Control masks and using his own authority as a Gym Leader to influence events, including funding a program that forces strength-boosting evolution upon weaker Pokemon, the Masked Man set his sights on the realization of a master plan years in the making that would gain him control of Celebi, thus allow him the power to control time itself. He came just an inch of success in the end, risking sending the entire planet through a Time Crash just so that he could travel back in time to reunite his beloved Lapras with it's parents that he lost in tragic accident so many years ago, the failure to properly grieve and cope with his emotions about this matter having gradually driven Pryce mad, but still just sane enough to design a thoroughly thought-out plan and implement it years later. Despite being a Misanthrope Supreme who deployed cruel methods and almost wrought irreparable damage upon the world, Pryce was a firm believer in loving Pokemon and doing anything you could for the sake of that love, and when his icy heart is finally reached and he realizes he was wrong, he allows Gold to return to the present day world even as he slips away into the time stream, encouraging him to live on for his Pokemon.
  • Team Galactic's leader Cyrus in the Diamond and Pearl and Platinum Chapters is a self-righteous Visionary Villain who is at once ambitious, intelligent, and well ahead of most other trainers in the Sinnoh region in terms of raw power and how he advances his goals. A firm believer in human potential, Cyrus felt that humanity could never complete itself and perform to it's highest potential so long as "incomplete" spirit lingered in the human heart, which gave him a desire to purge spirit from reality and remake the universe and all of existence into one that functions without it. Through careful planning, a series of tactical diversions, and sheer determination, Cyrus manages to stay one step ahead of the heroes, even Champion Cynthia herself, and succeeds in capturing the Lake Guardians, harnessing their power to create the Red Chains. When the second one was incomplete due to the Guardians' escaping, Cyrus had a weaker artificially-created Red Chain as a substitute. With the Red Chains, Cyrus takes control over Dialga and Palkia, forcing them to fight each other. The resulting clash will tear apart the Space-Time continuum, allowing Cyrus to create his "complete" world in its wake. Upon his defeat, Cyrus begins to see the error of his ways and later returns to assist the Dex Holders in taking down the traitorous Charon. Cyrus then departs alongside his loyal commanders to lands unknown, commending the Dex Holders for their noble and "complete" hearts. Stoic but polite and civil, Cyrus proved to be one of the series' most tactically brilliant and formidable antagonists.
  • The Black and White and Black 2 and White 2 Chapters features two leaders within Team Plasma, Ghetsis Harmonia Gropius and Colress, making their bids for this status. Ghetsis ends up a subversion while Colress plays it straight. What's particularly impressive is that it's Ghetsis who carries the air of an polite, collected, calculating Chessmaster while Colress, according to Blake, is childish, emotionally driven, and "not mastermind material", yet Colress ends up proving the far more savvy, intuitive, and unpredictable of the two. First appearing under the guise of "Hoodman", Colress makes it clear that his loyalty to Team Plasma is based only in his desire to further his research on what draws out Pokemon's fullest strength. He uses his Ice Drive Genesect to freeze the Swords of Justice and obtains what he believes to be the Reveal Glass so that he can use it on the three legendary force of nature Pokemon when he sends them out to battle the international police and their allies at the Unova League. Finding that what he has isn't the original Reveal Glass, Colress is still able to amplify the Pokemon's power and overwhelm his opponents while he makes his escape on Genesect, on which he uses cloaking technology to hide it's form from any spectators. Two years later Colress spearheads Team Plasma's war on Unova, locating the runaway Sage Zinzolin to press him for information before taking him as a captive and using his Mind Control machine to subdue Kyurem so that it can be captured and it's power may be used to charge the Freeze Ray that's unleashed upon Unova, with Colress taking great glee in the results of Kyurem's full power on display. When Blake and Whitley infiltrate the Frigate, Colress is quick to intercept them and have them frozen and tossed down into the sea. Keeping in close contact with Ghetsis but beginning to tire of the back-and-fourths with his "friend" who he recognizes is only using him for his talents, Colress soon acts against Ghetsis' knowledge by rescuing N when Ghetsis attempts to have him killed, deeming N too valuable and extraordinary a person to be wasted, which ends up playing into Ghetsis' undoing. At the Giant Chasm, Colress attempts to have Kyurem freeze the whole place solid with his enemies still inside, but when he learns that at that moment his device that keeps Kyruem controlled has been shut down, he rather cheerfully determines that Team Plasma is a lost cause and he must Know When to Fold'Em, making a hasty retreat. Even when Blake and Keldeo fight back against him and his Genesect, breaking the real Reveal Glass that Colress was holding onto in the process, Colress manages outwit and almost defeat his opponent, showing his respect when he's narrowly defeated instead. Amoral to a fault and dedicated only to his experiments and research yet also friendly and exuberant at almost all times, Colress believes that results justify the approaches taken to get them and proves smart enough to earn himself a more well off position than his employer even in prison.
  • Team Flare's leader Lysandre in the XY/Z Chapter is also a strong qualifier. A suave, intelligent, stylish and ruthless Sharp-Dressed Man of Wealth and Taste who runs Lysandre Labs and owns the Café in Lumiose City while secretly directing the terrorist actions of Team Flare, Lysandre showcases his morally grey character early in when he generously has Trevor's Holo Caster repaired while in the same scene threatening the boy when he starts to get too suspicious, and also displays the genuine respect and affection he has for Pokémon like his Gyarados. Using his Lysandre Machine to absorb Xerneas' life energy in order to power his ultimate weapon, Lysandre fights off opposition from the trainer called X by Mega Evolving Gyrados, seeing through X's ruse to drain the energy from his machine and free Xerneas, being not even fazed by Xerneas' appearance since he notes it's in Neutral Mode, before swiftly defeating X's best Pokémon. Following the collapse of the ultimate weapon and Flare HQ, Lysandre immediately sets in motion a contingency plan where he begins training with his Pokémon inside of a cave while his team begins taking Pokémon from the nearby village to put them inside Absorber Stones that drain their life energy, and capture the Pokemon Zygarde for him. Lysandre later manipulates Mewtwo into battling X and Blue so that it may be weakened enough to be captured, activating a device to summon Emma and Zygarde from underground, using a system to take control of them both. Even when his control is severed, Lysandre takes Zygarde's Poké Ball, making Zygarde his to command, and despite losing his own Mega Ring, Lysandre still comes dangerously close to realizing his vision of a more beautiful land rid of all "filth" and "parasites", even announcing to the entire Kalos region his plans to destroy everything with his new ultimate weapon when it seems there's nothing that can stop him from doing so.
• Pokémon Diamond and Pearl Adventure: Cyrus, leader of Team Galactic, has some of the qualifications for this down. As in the games, he's a brilliant minded Visionary Villain who's often thinking many steps ahead of the heroes, is able to rationalize his actions no matter how deadly as being Necessarily Evil for the sake of a better future for the world, and has just enough charisma to sway many into following his lead without letting any of them know that he the plans to literally destroy the existing world with by resetting time back to the universe's beginning using Dialga's powers and then creating a new one in it's place where all living things would be stripped of emotion and free will, and he'd reign over it as it's God. Despite being notably more emotional and unhinged than his game counterpart, Cyrus possesses self awareness of his darkest emotions and this keeps him motivated in his ambitions to rewrite existence so that it may be rid of such emotions. His battle prowess and dedication to his cause consistently manages to impress Hareta despite him knowing that Cyrus is in the wrong, and Hareta in turn both impresses and influences Cyrus enough for him to rethink his evil ways. When Dialga and Palkia's fight threatens to tear apart all of existence, it's Cyrus who divulges a working strategy for stopping this from coming to pass, and when he returns to lead his old followers in the charge against Charon, all of them get behind him without question due to how bold and inspirational a leader he is, despite the fact that he'd previously mistreated or even tried to kill them!

Stage Show

• Pokémon Live!: Giovanni, as always, is the charismatic leader of Team Rocket out to conquer the world. Building the MechaMew2 robot after failing to capture Mewtwo, Giovanni lures trainers to his gym with his Diamond Badge, having MechaMew2 copy various Pokémon's attacks and using them against its opponents. Having defeated hundreds of trainers with this tactic in a single day, Giovanni plans to use the attacks copied by his mechanical marvel to gain world domination. Also having had a romance with Delia Ketchum when they were teenagers, Govanni lures her and Professor Oak into a trap, kidnapping them to force them both to witness his victory. Luring Ash to him after acquiring his Pikachu, Giovanni easily defeats the Pokémon and orders MechaMew2 to kill Ash once in for all. Despite Mewtwo suddenly stepping in and saving the day, Giovanni still proved to be a cunning mastermind prideful of his own manipulation skills.