Magnificent Bastard/Multimedia/Pokémon

The magnificent masterminds of the Pokémon franchise:

Games

 * 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.
 * The Big Bad of Generation VII,, may be among the most successful and manipulative villains in the core series.
 * 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.
 * 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.
 * Team Rocket's Meowth, of all people, attempts to be this in the Best Wishes 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 the same series, 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 going to jail) get him down: he just vows to move on to a new approach!
 * 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.
 * Let's not forget Mewtwo's original persona from Pokémon: The First Movie. Let's see. Tries to Take Over the World (or just mass produce a whole race of Clone Pokémon to prove their superiority to naturally born Pokémon in the original version) in an outrageously audacious fashion, is almost never seen to lose his cool (and regains it pretty quickly once it's lost), quite the planner, charming in a calculating, suave kind of way, and, let's face it, was going to win until Mew showed up.
 * 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.

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, 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 Even the Gold/Silver/Crystal Chapter has her showing an epic case of Crazy Prepared when  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, 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 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  Despite being a Misanthrope Supreme who deployed cruel methods and almost wrought irreparable damage upon the world,  was a firm believer in loving Pokemon and doing anything you could for the sake of that love, and
 * 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, and as in the source material, 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. 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 end up in a more well off position than his employer.
 * Team Flare's leader Lysandre in the XY/Z Chapter is also a strong qualifier. Like Giovanni and Cyrus he's suave, intelligent, stylish and ruthless, and like Ghetsis and Colress, has a back-up plan that he launches immediately once his initial master plan fails.
 * Pokémon Diamond and Pearl Adventure:
 * Cyrus, boss 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, they 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!