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Spinnerette: Dr.Universe, wait! At least tell me something! You were a respected scientist, your work on the Cherenkovkirby Reactor was going to benefit all of mankind! Why would you turn into a supervillain? WHY?! Dr. Universe: I read anAyn Randnovel.
One Piece makes occasional mention of the World Government's top scientist, Dr. Vegapunk. He is one of the most speculated-upon characters in the manga. Apparently, he's an Omnidisciplinary Scientist, having created a cyborg with Devil fruit powers (Kuma), multiple copies of said cyborg armed with laser weaponry (the Pacifista), catalogued all known devil fruits, revolutionized the power of the sea as uses of Seastone, and figured out a way for inanimate objects to "eat" Devil fruits. For all this, events around the Time Skip have alluded to Vegapunk being morally ambiguous, and truly any statement of him being "evil" before then was an assumption. During the Time Skip, Franky, having burned off all of his skin, rebuilds his body using Vegapunk's technology
To a lesser extent, Gecko Moria's right hand man Dr Hogback, a surgeon of legendary skill who assisted Moria in creating a zombie army.
Vegapunk's rival, Ceasar Clown, is stated by all parties except his underlings as being evil and then, only because he shifted the blame for his own atrocities onto Vegapunk, and was arrested by the world government for sabotaging the science team's human experimentation. His arc shows thathis reputationisfullydeserved
Herr Doktor in Hellsing is the evil genius for Millennium.
Hakase in Mahou Sensei Negima! probably would have played this part in Chao's evil army if not for the fact that Chao was also an Evil Genius of an even higher degree. Still, this was essentially her role in that she was the one overseeing the ritual to remove the world's Weirdness Censor, not actually taking part in the battle
Naruto has Orochimaru with Sasori for the Akatsuki after Pain's death Tobi the Big Bad takes the role until Kabuto joins and is this for Tobi's akatsuk army.
In Mobile Suit Gundam Wing, Chief EngineerTsubarov was this to the Romefeller Foundation. A brilliant technician, he invented the remote-controlled Mobile Dolls whose useage consumes much of the subsequent plot; he's also one of the few men at the OZ base who realises that using the captive Gundam pilots as test subjects might be a bad idea. Curiously, he had a personality that one would more typically associate with The Brute being a thuggish Jerkass and Smug Snake who loathed pacifism, had No Indoor Voice, dealt with problems by applying as much brute force as possible, and went out in the midst of a truly epic Villainous Breakdown, ranting about how he was invincible.
The originalEvil Genius in a Gundam series was actually Princess Kycilia Zabi. She's one of the Principality of Zeon's better strategists and admirals, is in charge of Newtype research and the new mobile suits and mobile armours that come with it, and on top of it she's a Lady of War who's not afraid of getting her hands dirty if she has to.
Alister/Amalda was this to Dartz's group of henchmen in Yu-Gi-Oh!. Nesbitt plays this role to the Big 5, being their tech guy and weapons expert; oddly enough, he's perhaps their poorest duelist.
Darth Maladi from Star Wars: Legacy is both a Sith alchemist and the head of Sith Intelligence. She's generally portrayed as one of the most cunning Sith characters in the comic, but seems to enjoy her schemes and experiments more for their own sake than from the hope of doing anything constructive with them.
Also Vul Isen as he is believed to be a scientist. He never accepts anything without a proof.
In All Fall Down, IQ is VERY bitter about not being one of these anymore.
There are occasional subversions: Whitaker, Khan, Kananga, Drax, Kristatos, and Le Chiffre were all the "main brains" in their operations as well as the leaders, and Sanchez had what is nearly a parody of one named Milton Krest. Stromberg has two, both of whom he kills early in the film to cover his tracks.
Grand Moff Tarkin from A New Hope could count, as he has the Death Star, and is a strategist with his own doctrine.
And in the prequel trilogy era, Nute Gunray and the Separatist Council fit the role as they are the brain of everything, and later when they are no longer needed, they are killed by their boss.
James McCullen and the Doctor in GI Joe The Riseof Cobra. At the end of the film, the Doctor becomes the Big Bad, Cobra Commander, and turns McCullen into Destro.
Mystery Men's Casanova Frankenstein is an evil Disco genius. Even his archnemesis asks him for help with his quips. He wears a set of golden finger cuffs that carry sonic rays and hyper-lasers, and a pair of slippers that emit poison gas. And that's just what his enemy knows he's wearing while he just sits around in his dressing gown.
In A Fistful of Dollars, Ramon Rojo is a non-stereotypical example. In a family of archetypal Mexican banditos, Ramon is The Strategist, concocting the plan to steal the gold from under the Mexican army's nose, and orchestrating the eventual massacre of the rival Baxter family. He's also the only one to see through Joe, and keeps a wary eye on him throughout the film, eventually deducing that he is the traitor in their ranks.
Magneto. With truly amazing schemes. In X-Men: Days of Future Past, he was able to steal a file containing the details of the Sentinels, after reading it over he was somehow able to reprogram them while inserting metal tracks within the bodies.
Toad from X-Men. He's even seen tampering with Magneto's machine.
Barty Crouch Jr. is a better example. He replaces a teacher, kills his father, and lures Harry away from potential protectors, and no one realizes until nearly the last moment what he's up to.
Professor Moriarty, the Arch-Enemy of Sherlock Holmes, is described by Holmes himself as "a genius, a philosopher, an abstract thinker." Moriarty uses his brilliant mind to run his criminal organization,and, unlike many other evil geniuses, he is clearly the boss.
In The Witcher, we have Vilgefortz. He is easily the most smart and powerful wizard in the North, and he let it get into his head.
Tyrion Lannister from A Song of Ice and Fire, an educated, smart, and calculating dwarf sort of qualifies. However, he wasn't really an ally of House Lannister and he was enemies with Tywin. He embodies this trope in his own organization, in which he is also the Big Bad. He isn't really that evil though.
The Artemis Fowl series is full of these, which makes sense, since the protagonist himself is a Teen Genius, and that requires antagonists to match. We have Artemis himself in book 1 (in his status as Villain Protagonist), Opal Koboi in book 2, Jon Spiro in book 3, Opal Koboi again in book 4, Minerva in book 5, Opal Koboi AGAIN in book 6. Turnball Root in book 7, and Opal yet AGAIN in book 8.
Most incarnations of Power Rangers and Super Sentai have one of these among the villains, with responsibilities commonly including mass-producing Mooks and the Monster of the Week, making monsters grow, and generally being the one who knows the most about the finer points of the magic/technology of the season. In Power Rangers, the first and probably the most iconic among fans was Finister, the series' first monster maker.
Elizabeth from Wicked Science becomes a genius and she uses her new intelligence as a way to try to get money, fame and Toby's affections. The evil part is that she has little morals when it comes to use her inventions, including using a teleporter to sneak in Toby's laboratory so her goon can destroy/steal/sabotage whatever Toby is creating in the episode, or trapping him in a "Groundhog Day" Loop so he accepts the new universe in which he's trapped, where they are a couple and his friends hate him.
The campy 60's Batman series had lots of villains who were Canon Foreigners but one of the few who was entertaining enough to make return appearances was the Evil Genius Egghead, played by Vincent Price (who often commented publically how much he enjoyed playing the role).
In Magic: The Gathering, Yawgmoth is this and the Big Bad, but in New Phyrexia, with its five-color theme, Jin-Gitaxis, the blue praetor, takes this role.
Professor Hojo in Final Fantasy VII is this to President Shinra. After Shinra is killed, Hojo either remains the Evil Genius or gets promoted to Big Bad, depending on which side of the multi-faceted "who's responsible for Sephiroth's actions" debate you're on.
If this is what Hazama entails, then there must also be a mention of Relius Clover, a brilliant researcher who sought only perfection and has performed horrendous experiments and plans (as shown during his EX Story where he practically played Sector Seven and Kokonoe for chumps to create his Ignis). He just got less time to shine than Hazama though his inclusion as a playable character and a story mode for him in elevated him a bit.
Agnus fills this position for Sanctus in Devil May Cry 4. Although one could equally argue that he's The Dragon, as he appears to be the only member of the Order beyond Sanctus who truly understands what's going on, killing him is the last thing that needs to be done before the final confrontation, and the nominal Dragon is a Honor Before ReasonHero Antagonist.
Dr. Elvin Atombender from the Impossible Mission games is a genius computer programmer and former university professor. Although he has been unstable his whole life, he officially became criminally insane when a power failure caused the deletion of an artificial intelligence program that he had nearly finished. The player must stop him from hacking into the defense networks of the world's superpowers and starting a nuclear holocaust.
Strider has Herzog Schlange in Strider 2 and Professor Schlange in the HD Strider remake. Both are (mad) geniuses in charge of building the bizarre mechanical monsters and weapons used by the Grandmaster's army. In the latter's case, he's charged over the Grandmaster's entire research complex, and seems to be only below Juroung in terms of ranks. Though this didn't save him from being offed in the end.
The Grandmaster himself has shades of this, though he leans more toward genetic engineering instead of robotics, in his quest to create a new race to which replace "the sons of old gods" and rule Earth as a true God.
Dr. Kimaira in Tenchu: Wrath of Heaven, notably because he's a Mad Scientist who creates wooden automatons with hidden machine-guns in medieval Japan.
General Tarquin is sort of this to his own team of aging adventurers (nicknamed "The Vector Legion"). According to Word of the Giant, the other team members see him as the 'ideas guy', whose Genre Savvy allows him to come up with plans that a group of very powerful evil adventurers can all join in on for their mutual benefit without backstabbing each other. Tarquin himself thinks this makes him their leader. The others don't, but think he's useful enough not to press the issue. They also have two actual evil geniuses who takes care of all the actual planning and minutiae.
Wayward Sons: Doctor Chu, who very much enjoys performing torturous experiments on live subjects.
Elia of True Villains takes over most Evil Genius duties. Just replace technology with magic.
Tattletale fills this role in Worm, though it should be noted that she's not supersmart, instead her power makes her a master of the Sherlock Scan, which she uses to great effect in social, combat, and political situations.
Tarantulas of Beast Wars is this all over the place.
Cartman himself from South Park is this in "Scott Tenorman Must Die", where he tricked Scott Tenorman into eating his parents after calculating a painstaking amount of detail, up to Cartman's friends betraying him.
Xiaolin Showdown: Though he doesn't fit all of the character tropes, Jack Spicer (himself a self-proclaimed Evil Genius, with emphasis on self-proclaimed) calls Chase Young "the greatest Evil Genius in the world" and there's no denying that it's true. As for Jack himself - there's no denying that he is a genius, it's just whether or not he's actually, you know, evil.