The most badass, all-knowing masterminds in gaming go here.
Main antagonist Aken Bosch of Descent: Freespace 2 spends the entirety of the game attempting to ally with the Destroyers, AKA the Shivans (who happen to be Omnicidal Maniacs), whom he believes are unstoppable and will never be defeated regardless of the GTVA's efforts. When you are tasked with a squadron to intercept and disable his ship, he openly sends a communication channel to the player and taunts you and questions the competence of your commanders as he warps out of the system, well before you have any chance at hitting him, just before a Shivan fleet ambushes the player's squadron. He frequently outsmarts the entire GTVA command in his capital ship, and when it looks like he's finally been caught when his ship is disabled and boarded, it's found out that he had planned a ruse which included the capture of his ship and all of his crew all along, and he had actually used the confusion to escape alone on-board a Shivan transport. What happens next will always be a mystery, as the trilogy was never completed.
At least part of this was actually due to GTVA Command playing Bosch right back: they knew what he was up to with his secret project, and they wanted to allow him to complete it and then steal it from him. It worked. Whether Bosch got the last laugh depends largely on whether he managed to join the Shivans or was taken prisoner by them.
Blue Planet features Admiral Chiwetel Steele, who achieved this title after an absolutely stunning Batman Gambit that resulted in the complete annihilation of the player's squadron (whose nickname was the Wargods) in one fell swoop. Nobody saw this coming, and it took nearly the entire campaign for him to set it up, including playing off the gambits of two admirals on the opposing side.
The CO "Hawke" from the Advance Wars series. He is extremely manipulative and twists his circumstances to achieve his ultimate goals, which are not always obvious. In Advance Wars 2, he fakes his own death and kills his former commander, Sturm, after he is weakened by the final battle with the player so that he can take over command of the Black Hole Army, and in Advance Wars: Dual Strike, Hawke joins the player's side after Von Bolt decides Hawke and Lash are no longer useful and tries to kill them, with the ultimate result of placing him in control of Von Bolt's life-sapping device, which he vanishes with. He is calm, reserved, and ruthless, but his CO abilities, which heal his own units while damaging those of his opponents, reflect a surprising trait for a Magnificent Bastard: he cares about the fate of his own troops, and acts with his own brand of honor, making him also an antivillain.
The AI Durandal... Duranda, Durandana, Durandal, from Marathon. Even if Durandal caused the fight with the Pfhor, and in doing so, got a human colony almost completely wiped out (he made the survivors his soldiers), he pretends he's doing so to help humanity. Pretending to help humanity gets the humans to fight for him. In the end, however, he's just doing everything for himself, so that he can become God of the next universe, as Tycho points out.
"If you win, we'll continue our relationship on friendlier terms. If you lose, you die. Unlike Leela, I give no hints. Find the way on your own, or die trying..."
When he's obviously going to lose a naval battle of one ship against the strongest naval force in the galaxy, he decides to blow up half of it, just because he wants to be in their history books.
Durandal: I'd have erased my seven times table to see the look on Admiral T'Fear's face when he learned I could focus a plasma beam at three times the standard range his ships could.
Also, everything he does in Marathon 2 is just magnificent. From the way he upgraded his ship, to the way he helped the humans capture a command post, and how he faked his own death!
Krelian is likely the greatest of all Magnificent Bastards.
His partner Miang is even better, and far cooler. Krelian mostly works behind the scenes, experimenting on nanotechnology and plotting to rebuild God. Miang, meanwhile, goes straight into the thick of things, even when the protagonists are ultimately mostly bit players in her scheme. When she deliberately built Oedipal issues into Ramsus, solely for the sake of building him into a weapon for killing Emperor Cain, and then alternately treats him like trash and makes sweet love to him to ensure he fulfills his purpose, and succeeds in every aspect of her plan (well, almost every aspect, seeing as she and Deus die at the end), it's hard not to be left open-mouthed in wonder.
Arkham of Devil May Cry 3 plays all the sides against each other, in order to open the gate to hell.
Spider of Mega Man X: Command Mission is in reality manipulating X and company from even before they meet him in order to obtain the latest series Macguffin, under the guise of his Commander Redips identity, a high-ranking maverick hunter. Sure, the name reversal's obvious in hindsight, but it's sufficiently stealthy and well-executed that most people tend to miss it on the first go-round.
Actually, Redips is the one doing the manipulation. The real Spider was murdered sometime before the game began.
Alex of the Golden Sun series manages to manipulate 4 different groups of characters throughout the games, all to achieve a power higher than Alchemy.It doesn't quite work out, but there was a big enough cliffhanger at the end of the second one to imply it could've.
30 years on, he's moved on to manipulating entire nations.
Depending on which theory surrounding Amiti's birth that you believe in (that is, whether Amiti was planned or accidental), Alex may be the most magnificent bastard or just a bastard. The bastard part is never in question.
Saturos may play second fiddle to Alex's bastard-ery overall, but that doesn't mean he's not talking the party out of their MacGuffins (and confusing his own partner as much as the heroes) just fine on his own. And unlike Alex, he's not shy about following that up with a good old-fashioned beatdown.
Ocelot of the Metal Gear series, is one of the greatest magnificent bastards in all of fiction, casually playing every side against every other possible side, all while twirling his prized revolvers. Almost everything that happens in the series can be somehow traced back to him, and when it can't, it's usually because it happened before he was born. Reached Aizen level in Metal Gear Solid 4.
There's also Liquid Snake, who spends most of Metal Gear Solidposing as an old ally of Snake's and manipulating him while carrot sticking Snake the whole game as he tricks Snake into activating Metal Gear for him. He also survives multiple explosions, falls, and gunshot wounds all with the hammy British accent of a Shakespeare villain.
Killzone's Scolar Visari, who creates public support through his sheer force of will, who singlehandedly rebuilds the Helghast (a word he invented, by the way) state into a highly disciplined military state with him as an absolute leader, and who then invades the neighboring human colony of Vekta. Oh yes, and he has some of the greatest speeches in video game history.
Jade Empire has Master Li, who pulls off an astounding plan that seems too complex to be possible. Then, if you play through the game again, you can see how carefully he planned everything and manipulated everyone, making even the crazy complex scheme believable (of course, he had twenty years to do so, and they don't call him "The Glorious Strategist" for nothing).
It also has a character with the regal title of "The Magnificent Bastard" from the game's England analogue. Though he doesn't really fit the trope, being voiced by John Cleese certainly qualifies him for the magnificent part.
Sir Roderick Ponce Von Fontlebottom the Magnificent Bastard has the single greatest name in the entire game.
Frank Fontaine of BioShock started off as just a small-time smuggler in Rapture, but after the discovery of ADAM, he set the wheels in motion to take over all of Rapture. He charms the lower class and corners the market for ADAM, giving him a massive army of both poor citizens and ADAM-addicted splicers. Then Fontaine faked his own death, reappeared under an assumed name, and led his followers in a massive civil war that left Rapture in ruins. The game's protagonist, Jack, is revealed to be a Laser Guided Tyke Bomb created by Fontaine in order to kill Rapture's founder. Who is also programmed to die on command when the job is done so he can't come back and kill the man that created him.
Depending on your point of view, Andrew Ryan himself is a Magnificent Bastard.
Albert Wesker, proof that one can be an ur-Chessmaster and a physically overwhelmingBad Assat the same time. Plus, there's, ya'know, the fact that he's never actually lost at his Evil Plans. He never regrets a single life he takes or a single sin he commits. Conceited and power hungry, Wesker would do anything to become more powerful. He even pretended to act as The Dragon for Oswell E. Spencer, when he was really taking everything he had and making it all his own.
And in the first game, he threatened Barry Burton that if he doesn't do what he tells him, something terrible would happen to his wife and two daughters. Using family compassion against someone... unforgivable! The fact that he had no intention of actually carrying out the threat doesn't change how effective it was.
The Emperor of Final Fantasy II was the series' first Magnificent Bastard. Capturing the princess was just a ploy to assassinate Firion, and the tournament to decide who gets the real princess is just a trap for him when that fails. He manages to take over both Heaven AND Hell. He even has a trap in his castle that leads to the basement, presumably so no one can sneak up on him and assassinate him.
Kefka of Final Fantasy VI qualifies as this. Despite his numerous atrocities (poisoning an entire kingdom, enslaving a main character, blowing up the world, etc) you can't help but being amused by him. Whenever he is on screen, you know you'll be entertained. Plus, being the only Final Fantasy villain to suceed with his evil plot gives him props, especialy considering he did the whole thing for fun.
Let's not forget that Delita became King through marriage to a princess who was not actually a princess. In a world where blood trumps everything, a pair of commoners became the absolute rulers of the realm, through divine right.
In Final Fantasy Tactics A2, there's Duke Snakeheart, a somewhat loony Nu Mou Arcanist in Duelhorn that does not care if innocent people get hurt during Duelhorn's attacks as long as the job gets done, wants to do things his way, and even hires your clan at one point to protect him from punishment from his clan members, to which he says "...Heh, that went well." after he does avoid it. If that wasn't enough, he reveals himself to be the traitor of Duelhorn, admitting to leaking their plans and turning the girl that Maquis saved into a zombie just for kicks.
Also from Final Fantasy Tactics, we have Dycedarg Beovule, the protagonists' oldest brother. Dyce murders his father, manipulates much of the events from afar (traitor sellsword Gaffgarion was Dyce's man for a time), and murders his commander Duke Larg to become leader of the Order of the Southern Sky. It doesn't work as well for Dyce than it does for Delita, though, and once his lies are uncovered, he becomes a Unwitting Pawn to the true manipulators of the war, the Lucavi.
How can we forget Formav/Vormav? He's the mastermind behind just about everything the Lucavi do, second-in-command to Ultima, and even succeeds in bringing her back to life — by sacrificing himself at the last minute!. Magnificent.
Final Fantasy VII has Sephiroth. In the past, he was chucked into the Lifestream. It's implied that he planned to do that anyway, but he's still mad about it, so he conspires to get revenge on the person who did it by using polymorphed clones of himself to set up an elaborate sequence of events that ultimately gives him a nervous breakdown and renders him comatose. He gets better. Done with the protagonists, he hides himself so that the very Weapons meant to stop him do his dirty work. Destroying the barrier protecting him gets rid of the weapons. Defeating him just forces him to rely on TWO backup plans to come back to life, one of which simultaneously corrupts the Lifestream to his ends. Xehanort borrowed a lot from him.
Rufus also has some tendencies towards this, but it's taken Up to Eleven in Advent Children, where he outwits the Remnants — and Sephiroth by extension — for most of the movie, and gets away with it after he's discovered.
Final Fantasy IX had both Kuja and Garland, who together orcheastrate most of the events behind the game and are usually always one or two steps ahead of the heroes.
Final Fantasy XII brings us Venat due to the simple fact that everything the heroes do is just a part of hir plan. EVERYTHING THEY DO. As in from start to finish, Venat was always on top and won. The heroes are just lucky Venat was actually after a better world where the Occuria didn't control Ivalice and mankind was free from them. Lucky indeed.
Vayne Solidor: Cool, calm, smooth, collected, brilliant, devious... Vayne is the very definition of Magnificent Bastard. If Kefka is the video game industry's equivalent of The Joker, Vayne is their Lionel Luther.
Starcraft had Kerrigan. While a major character of the original game, she doesn't show her true magnificence until Brood War, an expansion pack nearly as long as the original Starcraft campaign. The entire length of Brood War is Kerrigan playing the Protoss and two competing Terran factions against one another in order to spread the Zerg to even more worlds and eliminate Zerg opposition to her reign. She pulls it off magnificently, betraying and/or murdering every named character, and setting up a massive Downer Ending.
While she belongs here, do remember that she left Raynor and Zeratul alive, not to mention the whole Duran-saga. Seems like she may have dug a grave for herself, although Starcraft 2 will tell.
She spared Zeratul because she thought living with the guilt of killing Raszagal would be a Fate Worse than Death for him. Killing Raynor wasn't an option, as he disappears post-"True Colors" and she had to deal with more pressing issues in the form of Raszagal and the renegade Zerg. In Starcraft 2, sparing Zeratul and Raynor probably saved her life-Zeratul learns that Kerrigan's death would lead to the Hybrids exterminating all other life, and forwards this information to Raynor.
Before Brood War, Arcturus Mengsk held that position. Seeming to be the great hero everyone waited for, and then he killed off an entire planet's population just so he could become emperor.
Duran (or at least the unknown powers that stand behind him) is also hinted to be a Magnificent Bastard — or at least a Chessmaster. He certainly was a Magnificent Bastard when he was working for Kerrigan: he tricked her into thinking he was an Infested Terran to become her right-hand man, a position he used to speed up progress on Protoss-Zerg hybridization experiments. She never suspects a thing until he the moment he disappears.
Command & Conquer has Kane, the granddaddy of them all. Unshakeable, unflappable, and utterly in control the entire time (well, most of the time, anyway), for all the games, and also quite Affably Evil, Kane betrays his second in command, manipulates GDI to get what he wants (multiple times), is a veteran and master of Gambit Roulette, and in the latest installment, starts the Third Tiberium War just to get GDI to fire a Ion Cannon strike on Temple Prime, detonate a liquid Tiberium bomb, and call the Scrin to Earth. All so that he can hijack the Scrin gateway and leave Earth.
It gets even more awesome in Kane's Wrath. Not only does Kane manipulate the fractured Brotherhood into reunifying in the wake of Firestorm, he also engineers the rise of Redmond Boyle, who he wants to be in charge of GDI so he can manipulate him into using the Ion Cannon on Temple Prime. And he does all this while constructing LEGION, the ultimate strategic AI to interface with the Tacitus and bring him and Nod one step closer to ascension. And this is while fighting off the most well-armed and elite forces of both GDI and the Scrin.
And in Tiberian Twilight, he finally succeeds at his overarching goal: ascension.
Strangely enough, a droid plays the role of Magnificent Bastard in Star Wars: Knights of the Old Republic II. The first HK-50 droid you meet orchestrates the systematic murder of every single person aboard the Peragus II mining station (save for the imprisoned Atton Rand) and lockdown of the same facility, as well as several events preceding your arrival there, and administers a sedative meant to keep you unconscious until it can deliver you to the Exchange for the bounty on your head. Its plan works so smoothly, in fact, that even after waking up, you have no means of escape until T3-M4 intervenes.
Really, though, the true crown of Magnificent Bastardry should go to none other than Kreia. You can't get to the end of the game without simply being awed at how completely and absolutely she used and manipulated the Exile, with the implication that the Exile was fully aware the entire time that he/she was being manipulated but unable to do anything about it. Not to mention how she utterly and completely crushes Mandalore, Atton, and Hanharr psychologically.
And let's not forget Kreia trainedRevan, and was probably ALSO manipulating Revan for a lot longer and in-depth than she had Exile! She's also the only one who seems to know anything about the "True Sith," and mind-wipes Mical when he discovers a pattern to Revan and the Triumvate's attack patterns! Given that, it's not too much of a stretch to guess she may have been "the Sith" that convinced Mandalore the Indomitable to go on his crusade, meaning she would have been the Chessmaster behind at least 20 years of galactic history!
Another Magnificent Bastard droid: G0-T0. It's originally just a standard droid used to help with reconstruction after the last war, but got a Logic Bomb after the fact that it can't reconstruct the Republic without breaking its law. So, it broke free, and by just using holograms, managed to fool everyone that "Goto" the person really existed, and then go on to create a criminal empire that will help the reconstruction of the Republic. Remember that it's just a pretty normal droid, not a specifically constructed one.
Actually, G0-T0 was a specially created droid. If you'll recall, there was a quest early in the game about finding a stolen droid that was crucial to the whole rebuilding the planet thing; this droid had special programming and whatnot to do its job, making it nearly irreplaceable. And they mention that this droid was a replacement for an even better one that had mysteriously vanished — which you later find out is G0-T0. That's why he went rogue: he had such advanced AI that he deduced that the only way to save the Republic was to break the law.
However by sending the HK-50 after the Exile on Peragus II, this ultimately lead to the destruction of the mining facility and nearly doomed the entire Telos restoration project, which relied on Peragus for fuel. Given that the success of the Project would undoubtably help restore the Republic and that is what G0-T0 wanted to achieve, all he succeeds in doing is really screwing the pooch! Not to mention he orchestrates the Bounty on their head as a ploy to get the Exile to agree to work for him, which they point out they might have done if he had just asked! When you tally it all up, he might be a Magnificent Bastard, but he's downright incompetent!
M. Bison (Vega in Japanese) in the Street Fighter saga pretty much fits the bill, mind controlling multiple heroes, making them fight each other, having clones of himself to activate once he dies, and arranging the whole friggin' Street Fighter tournament just so he could make all those who want his head to beat each other up for him. Of course, he meets his end in the hands of Akuma, but it's not like death would slow him down. He's such a Magnificent Bastard that he manages to retain his awesomeness in, of all things, the Street Fighter movie... though only the first one. Legend of Chun-Li, not so much... even magnificence has its limits.
The Gravemind from Halo, for the way it manipulates everyone around it, combining complicated Gambit Roulettes with skin-crawling psychological warfare. Most striking is the way it ended the war with the Forerunners by turning the AI created to destroy it into its greatest ally using nothing but logic. Even when defeated, its only response is that its destruction is nothing but a temporary setback. And it does all this while speaking in poetry.
The Forerunner Saga expands on this; it's implied that the Gravemind is actually a multi-million-year old Precursor, or at least one's personality and memories, who was part of or planned a massive-scale Batman Gambit: seeding "Flood-dust" around the galaxy in capsules inside ancient warships, knowing, when humans found them millions of years later, they'd test it out on something organic, which would eventually cause humans to become infected; then, allowing humans to "beat" the Flood, hiding its real goal: gather enough forces to eventually assault Forerunners. All of this so they could test Forerunners' worth to hold the "Mantle", a position to guide the other races of the galaxy. And it's not even over yet; knowing that Forerunners would fail, they arranged for another species to be tested: humans, scheduled for 100,000 years after the Flood war, in the 26th century. It also gives a possible reason as to how he can manipulate and predict so much: his kind made humans, Forerunners, and the species of the Covenant. He'd know everything about us.
Master Albert from the Mega Man ZX games is one hell of a Magnificent Bastard. He fits the criteria like a glove, manipulating the entire cast of the two games for centuries. Even during his defeat, he doesn't throw any tantrum or scream/evil laugh at his defeat, he merely acknowledges his defeat and delivers one of the finest lines even spoken in the series.
Mind you, there's another person who could was potentially even more of a Magnificent Bastard than Albert - Master Thomas. In the hidden ending, he reveals that he simply helped the heroes (simply by making the defeat of Albert an official mission) for the sake of making Albert kick the bucket so Thomas could start his own scheme to reset the world, and even recruited the four rival Mega Men. It's possible that he planned Albert's demise from the beginning, thus manipulating the entire heroic cast into doing exactly what he planned. Which would make this one a Gambit Roulette that even Light Yagami would quite possibly be jealous of, considering both of them enacted over a span of 200 years. That makes this an example of a Gambit Roulette being designed to destroy another. That is truly magnificent.
It's implied that neither Albert nor Thomas is behind it all. No, it's very possible the Man Behind the Man is Model W. Aka Dr Weil. That's right, death has transformed ol' Kool-Aid man into the supreme manipulator behind Master Albert and Thomas, effectively beating Dr. Wily's track record. It's about time he added "magnificent" to his overwhelming bastardry!
Wily deserves a spot here. He's been hijacking games before Ganondorf did. Let's review his track record:
In "3" after trying to take over the world twice he manages to convince everyone, even Mega Man and Light, that he has reformed and that building a giant peacekeeping robot of death would be a great idea. Afterwards he reprogrammes 8 new robots built by him and Light, in order to steal the crystal needed to power up Gamma to Set up a pretty clever Xanatos Gambit: either Mega Man dies fighting them, so that he'll get the crystals with no one to stop him, or Mega Man wins but Wily still gets Gamma.
in "4" he kidnaps Cossack's daughter to blackmail him into killing Mega Man. Easy supplies with barely any cost to him if he loses and while Cossack distracts Mega Man and the world thinking he's dead, he's free to build up more resources so even if he loses to Mega Man here he still has enough resources to keep fighting.
In "5" he frames Protoman, then kidnaps dr. Light, depriving Mega Man of his two most trusted allies with the added bonus of emotionally tormenting him so he can't fight. Darkman allowing darkman to kill him. And if Darkman succeded in killing Mega Man everyone would think it was Protoman and He would have a harder time Fighting Wily. in 6 Though his disguise was terrible, he managed to make a fool of Mega Man, Light, Proto Man, and entire countries by putting on a beard and sunglasses. Compare his plots to other 8 bit villains plots, keeping in mind that he is just an old man without superpowers and yet he manages to pull this off.
In "7", after all of this, he just spends 6 months in prison due to having a backup plan: blowing up the prison with an army of robots he had in store. Then he plants his new robots Bass and Treble as Heel Face moles to gain access to Dr. Lights Lab.
In "9" he manages to convince everyone that Dr. Light is trying to take over the world and he can fight his evil robots, after Wily himself had tried to takeover the world at least seventeen times already. He reprogrammed Light's bots (who were going to be scraped due to a new Law, which Light was against) so that everyone would think Light is doing this as a protest.
He even held a TELETHON TO GAIN FUNDING, and managed to make EVERYONE except the main character FALL FOR IT. He managed get good publicity after at least numerous tries at world domination.
In the manga he walks up to Light, gloating without being dumb enough to give him enough info.
in 10 he manages to fool everyone, even the main characters, and in a meta sense some gamers in real life, that he was innocent again, setting up another Xanatos gambit: Mega Man and Proto Man would fight off the robots then get infected while he and Light would make the antidote so when the time comes he would have the antidote then force the world to surrender to get the antidote while Mega Man and Proto would be infected and go crazy forcing them to be shut down or killed. he only lost because he forget about Roll.
in short if you compare him to Bowser and Ganon back in the 8 bit era, you'd be impressed that a harmless old man with no powers did more damage than both of them and hijacked more games than the supposed God of Villainous Scheme Hijacking.
There's a whole bunch of Magnificent Bastards in Super Robot Wars over the years, but the biggest was, without a doubt, Commander Laker of the Far East Brigade, a character who never actually fights. Between being the planner of the campaign against Aeidoneous Island — which crippled the DC movement, helping plan the defence of Geneva from the DC's remnants, and the L5 campaign, he certainly is a competent leader. The icing comes on the cake, however, is the fact that before the DC War began, he gave the Kurogane to Elzam Braunstein, a supporter of the DC movement who promptly used it battle against Laker's own subordinates. Of course, come Elzam and company's Heel-Face Turn, the Kurogane gets one too and serves as the heroes' "shadow", stepping in and helping when things look hopeless, and getting supplies from Laker and the Far East all the while.
Aside from that, there's also Ingram Prisken, who on top of infiltrating the EFA way back before the events of the game even starts, helps put together the best team of mecha pilots in the world, trains the SRX team, and then makes a Face-Heel Turn for the purpose of motivating the team into becoming strong enough to not only defeat him in his transformed, stolen, and extremely powerful mecha, but also to become strong enough to defeat Levi Tolar in her Judecca. The defeat of Judecca deeming their race a dangerous enough threat to wake the Adjudicator to destroy them, and thus the team was suitably motivated to become powerful enough to defeat that, and fulfill the biggest Gambit Roulette of the game.
And now 2nd Original Generations has topped even that with Euzeth Gozzo, who not only was the man behind almost everything that has happened in the OG continuity, is explicitly aware of the experiences of his incarnations in Super Hero Sakusen, Super Robot Wars Alpha, and the Divine Wars anime, because when Euzeth is defeated, the Cross Gate Paradigm System moves all of his memories to another Euzeth in a parallel universe. He developed this safeguard to make sure that his Evil Plan of assimilating technology from the various continuities to increase his own power was almost impossible to thwart.
Manfred von Karma and Kristoph Gavin are quite worthy of this status for playing magnificent long-term gambits to ruin other people's lives. Matt Engarde also deserves a special mention for being able to pull a brandy sifter out of nowhere during his Reveal. Whilst in police custody, no less! Sure, all the villains in this series get their comeuppance, but some of them were just better at getting their evil ways before their eventual Villainous Breakdown.
Luke Atmey manages to set himself up as an Ace Detective while at the same time keeping afloat and benefiting from the thief he's hunting. He then falsely gets himself indicted for being the thief to keep from being convicted for his real crime of murdering a CEO. Then the only reason he's even caught is a slip of the tongue, and this is after successfully having four of the five crimes he was on trial for proven to have not been his doing.
Calisto Yew's interrogation behavior firmly puts her in this trope. She's able to slide off most accusations with either a bored stare or a fit of laughter, and even though she eventually breaks down, she doesn't really break. In fact, rather than surrender after her confession, as every other villain does, she pulls a gun out to escape. Twice. She was the one who infiltrated the Yatagarasu and destroyed the group from the inside out.
Then there's the Big Bad of Investigations 2, who managed to be the Man Behind the Man for everything in the game, all while doing such a good job of passing himself off as a Shrinking Violet even Edgeworth was fooled the first time they met. He orchestrated an extremely intricate plan to get revenge on three people, and when he finally drops the facade he shows he's more than capable of matching Edgeworth in a battle of wits.
Also, one of the gods in Elven mythology is named Fen'Harel, "the Dread Wolf". The elven gods were divided in two factions, the Creators (good) and the Forgotten Ones (evil): Fen'Harel managed to convince both that he was one of them, and tricked them in believing that the other faction would have won the war, unless they listened to his advice; by doing so, they were sealed away (the good ones in "the Heavens", and the evil ones in "the Abyss"), preventing them from interacting with mortals, and leaving Fen'Harel as the only god with the ability to impact the mortal world.
While she only has minor, but vital roles in both games, it is made very clear that you never want to interfere with any of the many schemes of Flemeth. Her accomplishments include: Somehow managed to absorb a demon instead of being possessed by it, gives birth to daughters only to steal their bodies to extend her own life, seals part of her soul in an amulet as she anticipates being slain to be reincarnated years later by an elven shaman who owed her a favor, and had a really good plan to become a god. And she most certainly has the attitude to not make anyone doubt in the genuis of her hidden plans.
Xemnas qualifies in 358/2 Days, and when you think about it, KH II, as well. Xemnas was the driving force behind the entire plot of the former, and played some serious Xanatos Speed Chess in the latter. The whole time in KHII, Sora could only do exactly as Xemnas wanted, and knew it. Every time Sora killed a Heartless only brought Xemnas that much closer to his plan. No wonder Saix stabbed Axel in the back and joined up with him....
Maleficent could also qualify in this series. She does evil with style, is very manipulative (especially in the case of Riku), and throughout the story, she's never really suffered any great defeat; only setbacks. Even after she herself was manipulated for Xehanort's plan, she was able to regain a castle and control over the Heartless in KHII by allying herself with Sora and the others, thus ending the game getting exactly what she wanted.
Master Xehanort of Birth by Sleep. He manipulates Terra, Ven, and even Master Eraqus into doing exactly what he wants, all the way up until the end of the game. And even after the heroes derail his plans in this game, he continues to be a threat throughout the whole rest of the series by proxy.
As of the latest game, Xehanort's gambit involves his heartless, his nobody, and hisyounger self.
Really, Kingdom Hearts has a bunch of Magnificent Bastards stabbing each other in the back. Marluxia had planned to get assigned to Castle Oblivion and raise up Sora with false memories to take over the Organization, but Xemnas and Saix knew about it from the beginning, so Saix has Axel derail this conspiracy. Axel also removes Zexion as a potential threat on the side. Saix had an even more well-hidden agenda, but it didn't work out so well for him. Vanitas is quite cunning himself, and most likely his plan was to backstab Xehanort and take Kingdom Hearts' power for himself once he had the X-Blade. Hades had no less than three separate plans to take over Mount Olympus, and largely didn't really care about Maleficent's little club.
Etna from Disgaea takes Enigmatic Minion to glorious new heights. By the time she's through OutGambiting a Big Bad who was blackmailing her, he's literally on his knees weeping and pleading for his life. What's more, she does a masterful job of annoying motivating Laharl to become a competent Overlord while hiding her true nature and motives from everyone. (The player included if you don't find her secret diary.)
While he's more of a Guile Hero, Seraph Lamington from the first game, Hour of Darkness, used Vulcanus as an Unwitting Pawn in his plans to bring peace between Celestia, the human world, and the Netherworld... which makes it even more magnificent! Not only is he always calm and stoic as well as polite, never raising his voice nor getting mad, he manipulates Flonne into waking up Laharl, that while making her think she was sent by him to assassinate King Krichevskoy. He knew all along that Vulcanus was using the Earth Defense force as well as other angels to attack and terrorize the Netherworld and hurt innocent demons, and chooses not to do anything about it but instead let Laharl, Etna, Flonne, and Captain Gordon prevent the attack. When Laharl and his two accomplices arrive to take over Celestia, he welcomes them and reveals every detail of his plans to everyone, to Vulcanus' shock. And what's even better? He pulls off a You Have Outlived Your Usefulness on the corrupt angel by punishing him with the Humiliation Conga of turning him into a flower (or a frog in the anime if you prefer) for the pathetic monster Vulcanus truly is once the villainous angel himself gets a Villainous Breakdown and tries to kill him.
Then again, as leader of Celestia, it is his right to punish angels who cause taboo in Celestia itself by turning them into harmless objects. He knew that Vulcanus was making pacts with Netherworld demons anyway, which was a taboo in Celestia. Interesting to note is that, despite his stoicness, he was also so remorseful for manipulating everyone, as well as the grief he caused both Etna and Laharl by turning Flonne into a flower for killing one of her fellow angels, that he chose to punish himself for said sins, and was willing to accept said punishment courtesy of Laharl himself, who was filled with the Unstoppable Rage to fulfill the Seraph's punishment. Of course, Laharl spared him, knowing that Flonne would've stopped him if she weren't turned into a flower anyway. To make the two feel better, and to make himself even more magnificent, the real punishment Lamington was giving Flonne was actually to make her a fallen angel. And in the credits played for this best ending, after finally being recognized as Overlord, both Laharl and Lamington shake hands as a sign of peace between both Celestia and the Netherworld for their hard work. Great work, Seraph.
If anything, Ghaleon's magnificent bastardry is even better in the sequel. Having had a change of heart during his death, when Zophar resurrects him to serve as The Dragon, Ghaleon secretly starts working on the plan to destroy Zophar. To this end, Ghaleon frequently appears in front of Hiro's party, mocking/threatening them while always leaving a small chance for them to escape. It is only after Ghaleon fights Hiro's party on purpose as the final test and gets defeated that Hiro realizes Ghaleon has been helping them all along. In the second playthrough, it becomes increasingly obvious just how Dangerously Genre Savvy Ghaleon is and how he follows the mistakes illustrated in Evil Overlord Liston purpose to help Hiro's party and not blow his cover. It still was not nice (hence the bastard part), but magnificent? Oh yeah.
Requiem: I cannot say that you will have gained my respect, but I will acknowledge that you fought well. Drink deeply of your success. Bask in the adulation of your peers. Savor this victory. Know that you have saved your world and this moment from the shadow of history. But you have only saved it for now. Do not think that you have saved the world for your future. Know that you have saved this world for my coming Dominion.
But the undisputed king of them all is Nemesis. Looks like a goofy Steam Punk villain, but is somehow responsible for nearly every development in the game world for the past hundred years (and even more so if you believe the Epileptic Trees).
Tales of Xillia offers us a very brutal deconstruction of this trope with Alvin, who shows us just what kind of toll being a Magnificent Bastard without also being a sociopathic chessmaster would probably take on someone. He satisfies every single one of the trope's requirements, from being charismatic and suave to underhanded, manipulative, and always looking out for Number One... The problem is that he justdoesn'thave the sheer callousness required to pull it all off, and each one of his betrayals and manipulations become increasingly more ridiculous and obvious. All his failures to be one culminate in a Villainous Breakdownthat results in him almost killing a fifteen year-old girl who was just trying to keep the group together and a near-crossing of the Despair Event Horizon. It's after this that he truly starts to embrace Character Development by ditching his treacherous nature and starting to actually become a responsible member of the group.
The World Ends with You has Yoshiya "Joshua" Kiryu. Certainly he fits with intelligence, dubious morality, and punch-in-the-face obnoxiousness ("Good going, Neku.") What makes him a magnificent, manipulative bastard, though, is the entire ending, and every single Secret Report. He is the ultimate Composer, with the power to resurrect people, steal memories, and generally screw with everyone's heads while hitting stuff with game breaking power and having, among other things, clairvoyance. Even the Higher Planes, the great heavenly powers that rule over everything, can't predict this guy, and his powers of manipulation are so great that even after revealing that he murdered the protagonist and manipulated him into possibly destroying his entire home town, and even with all the trouble he's caused, Neku doesn't shoot him. So he follows that up by shooting Neku, and he still manages to get out of that with the guy's trust in the end, and with making everything all right. Actually, he managed to plan things out so that just about everybody came out of it for the better, except of course for the guy he was competing against in the first place. A complete asshole — which is why we love him.
World of Warcraft honorable mention: Drakuru. An ice troll who is friendly enough to talk to you and actually genuinely appears to like you. He came out of nowhere, was trapped in a cage as a lowbie mob, and without leaving his cage or really telling you much of anything except he had a cool idea and wants to learn some stuff, manipulates you into taking down the entire Drakkari empire. By the time you get to Zul'Drak, the trolls inside are almost all dead or killing and eating their own deities in a desperate attempt to stave off the Scourge. Yes, you just took out the strongest remaining non undead native faction to Northrend. Oh, and they're also undead now and didn't really get much chance to fight back. Of course, Arthas had to pick up his villain ball and kill him in a totally pointless You Have Failed Me moment. He was one of the best characters introduced in this expansion, and now he's gone.
Drakuru is very much Affably Evil as well. When he gets his "reward" from Arthas — death and resurrection as a powerful Death Knight — he offers you the same "benefit" as your reward for helping him gain the position. When you turn it down, he doesn't get pissed off and try to strike you down, but instead, acknowledges your choice, thanks you for your help, and gives you a very nice piece of equipment.
Given the shadiness of some of the things he asks you to do, he can't hold a candle to Loken. Just about every stage of your unwitting complicity in his plan involves you doing nice things for people — rescuing an enslaved innocent, repairing relations between a bereaved demigod and his former friends — and half the time he didn't even have to tell you to do it. Then the last Watcher remaining at large and uncorrupted is captured by Yogg-Saron as you look on, helpless to do anything to stop it and knowing that you made it possible. Pity he then forgot the Evil Overlord List prohibition against "laughing at him then leaving him to his own devices".
While Kil'jaeden usually prefers to do things Chessmaster-style, he did get up close and personal with the orcs. He studied them for years before slowly misleading them with false visions and promises of power. They were so enthralled that eventually he was able to appear before them in his true form and almost no one noticed or cared that he looked exactly like the people they were killing because he told them to. And he made such a smooth transition from "this is the will of the ancestors" to "the old ways are weak and worthless, bow down to me now" that no one realized what was happening until it was too late.
Deathwing was presented as a Wicked Cultured villain in Day of the Dragon, Tides of Darkness, and Beyond the Dark Portal. He infiltrated Lordaeron under the guise of Daval Prestor in ana ttempt to destroy the Alliance from the inside, manipulated the Horde into finding the Artifact of Doom that he could no longer use, and nearly got his nemesis Alexstrasza killed from too much forced breeding, without ever getting his hands dirty. By the time the Cataclysm expansion for World Of Warcraft rolled around, though, he had become an Omnicidal Maniac because of the Old Gods.
Reaver in Fable 2 manipulates people into giving up their youth and beauty so he can be immortal. But in Fable 3, he really takes the cake. Becoming the evil path advisor when you're king, whether your decision is for or against him, Reaver Industries takes all the credit for the changes in Albion. Oh, and he becomes an advisor even after he tries to kill you. If that's not enough to make him magnificent, he's voiced by Stephen Fry.
Ash Crimson of The King of Fighters has been manipulating every single one of his teammates since day one. He chooses his teammates based on the best ways to manipulate them. Oh, and did we mention that he's managed to steal Chizuru Kagura's and Iori Yagami's powers. Yes, you heard me: a gender-bending Scrappy kicked the ass of one of the most popular characters in King of Fighters. To add to the humiliation, Iori got his ass kicked while in Riot of the Blood mode, which makes him stronger. Proof that Ash is Obfuscating Stupidity. One can only wonder how he's going to take Kyo's powers...
In KOF XIII, it was revealed that he was manipulating every single person in and outside the tournament, whether they are directly involved in the plot or not. He had used the tournament and its participants to keep everyone distracted. He had brought out Elisabeth, whose lineage revolved around eliminating the Big Bad. He had fed information to Adel, which in turn gave the information to Heidern, who was already investigating the case with the help of his team, K's team, and undercover agents. He slipped out a piece of information to NPCs who are implied to have sabotagedSaiki's schemes. And that part of him stealing two of the sacred treasures? Turns out that was his plan to keep Saiki contained inside of him... and ultimately, getting himself and Saiki Ret Goned. All to protect Elisabeth, who not only is the sworn enemy of Saiki due to her lineage, but Ash's Only Friend since childhood. Therefore, whether Ash is this through and through or a Guile Herowilling to put on a massive Jerk Ass Facade no matter what he truly feels (and King, Athena, and Chin notice his inner turmoil at some point)... it's ultimately up to the player.
And before Ash even showed up, the game already had examples of this. The biggest ones were Rugal Berstein (a stinking rick Arms Dealer and Adel's father who hosted the first two tournaments purely to find the strongest fighters and fight them to his heart's content to later make them into statues) and specially Leopold Goenitz (the Herald of Orochi who cracked the Seal on him via killing Chizuru's sister Maki, controlled Leona into killing her fellow villagers as punishment since her dad refused to help him, is implied to have recruited the New Face Team, took out Rugal's eye years ago and is the SNK Boss from KOF 96 — all of this, with incredible flair and style.
Albert Silverberg of Suikoden IIIconstructs the entire plot of the game single-handedly and then casually derails it, confident that he's proven his genius and increased his reputation as a strategist.
To sum up: Meet The Spy shows that he can kill an entire enemy team in various ways, from slicing the Sniper to ribbons to snapping the neck of an enemy Medic, he shows that he can seamlessly transform into anyone he wishes...and he's banging the BLU Scout's mum. The BLU Spy also shows how Crazy-Prepared he is, having the folder with these incriminating photos in on hand purely so that he can make the perfect Your Mom joke, and to top it all off, the Spy appears to be charming and suave, almost James Bond-like. Magnificent, indeed.
Mario series: Paper Mario's Dimentio. This guy manages to nearly bring about The End of the World as We Know It without ever really needing to lift a finger, and even kills Mario, Luigi, Peach, and Bowser in a fantastic subversion of No Sneak Attacks that comes out of nowhere, and is only really hurt by the fact that they got better. Granted, that was part of the plan, and things were set up to still go through even if he himself was defeated.
He doesn't kill them, he merely sends them to the Underwhere alive. But considering that he fakes his death and comes out of nowhere with another sneak attack that, if Nastasia had not jumped in front of, he would have easily succeded, and secretly placing a mind control device on Luigi as he fakes a Taking You with Me.
The main villain of Mario & Luigi: Dream Team. Antasma and Bowser team up early on, clearly just for convenience. The inevitable betrayal? Antasma never saw it coming. Bowser played the entire cast throughout the entire game to reach his goals.
Kirei Kotomine in Fate/stay night. Only really prominent in Heaven's Feel route where you know perfectly well he's a bad guy and even Shirou knows. Lancer dies, the Grail changes hosts, Zouken Matou is involved, Gilgamesh gets eaten, and dozens of other cards are going against him, and he still makes it to the final fight after beating Zouken and True Assassin at the same time. His Xanatos Speed Chess skills and utter truthfulness throughout the game even make his mullet forgivable.
In the greater Nasuverse history, it is possible that the most magnificent of Magnificent Bastards is Kishua Zelretch Schweinorg the Wizard Marshal. Even if indirectly, or through other people, he's pretty much had some influence with everyone in the series. He killed Brunstead of the Crimson Moon, helped raise Arcueid, is trolling the Mage Association and the participants of the Fuyuki Grail Wars, which he started by jury-rigging a potential link to the root of all things and knowledge, the Akasha, and travels alternate dimensions, among other things.
Ovan from .hack//G.U.. Not only is he the real Tri-Edge, he P Ked Shino, is responsible for the infection of AIDA, gave Sakaki the AIDA cores required to turn himself and others into coma-inducing P Kers and has been manipulating Haseo, along with the Twilight Brigade and the members of G.U., since the very beginning with the purpose of defeating and killing himself just so he can cleanse the system of the virus and free his little sister from his arm along with bringing everyone back from their comas.
Fire Emblem has Naesala, that lovable victim of Chronic Backstabbing Disorder. He betrays people in ways that for anyone else would be well beyond crossing the Moral Event Horizon... but he is just so masterful that characters (and fans) are willing to look past it. It reaches the point where he gets a Blood Knight telling him It's Personal to leave, by convincing him that there is someone else with a higher right to his head (which, admittedly, is true)... then proceeds to get said someone else not to come after him simply by becoming Sanaki's bodyguard, meaning that if Tibarn (the aforementioned someone else) kills him, he will face the diplomatic wrath of the world's most powerful country. And this move kills two birds with one stone for him by letting him abuse a loophole in his contract with Begnion, thus allowing him to betray Lekain... who has no idea about any of this until Naesala decides to casually inform him, a move that is timed right before Naesala brutally kills him. And all of this is just him in Radiant Dawn. It isn't even touching his manipulations in Path of Radiance.
Naesela in POR: He has his country work for Daein as if they were a common mercenary group, though Naesela is secretly a Double Reverse Quadruple Agent who is merely trying to protect the heron prince and princess, Reyson and Leanne, from being abused by Daein.
NOTHING can compare to Lekain himself, Vice-Minister of Begnion and head of the Begnion Senate. He orders the assasination of Apostle Misaha and blames it on the herons, causing the Serenes Massacre which burned the forest and killed all the herons except for two princes, a princess, and the king, though Rafiel got lost in the desert, and King Lorazieh fell into a coma. Not to mention ignite Lehran's loss of hope in the Created. 25 or so years later, he installs the five-year-old Sanaki as empress so that no one higher up than him would learn of his abuses in laguz slavery, or that he had Sanaki's elder sister, the true apostle, murdered along with Misaha (though it turns out to be Micaiah in the end). 5 years later, he orders Numida and Jarod, the commanders of the Begnion Occupational Army, to abuse Daein in any way they see fit, similar to what Stalin did to Eastern Europe after World War II. And 3 MORE years later, Lekain imprisons both Sanaki and Sephiran so that he could order the extermination of all laguz on earth in the war with the Laguz Alliance. He also enacts the blood pacts he has over Kilvas (from a century ago, but not made by the current senate or Kilvan royals, but by a couple previous generations) and Daein (due to the workings of the Daein-born senatorial double agent and creator of the Feral Laguz drug, Izuka, creating a pawn out of Pelleas, who was not Ashnard's son, to become king of Daein. The real son was Soren, who didn't even know it himself), so that they would fight alongside the Senate and destroy all "Sub-Humans", with the coup de grace being the murder of Sanaki blamed once again on the herons. Luckily, that was all stopped midway, with Sanaki's escape from Mainal Cathedral. And when Ashera casts her judgement on Tellius, Lekain leads the Disciples of Order to kill all your guys under the delusion that "the false apostle and her minions are the servants of the dark god, and we (the Order) are the will of the holy goddess Ashera herself". And he even leaves Numida to die in the Grann Desert when the Dawn Army made their approach there. And in the end, it turns out he really knows NOTHING of the truth, and that he believes his delusions are actually the truth. All those monstrocities he caused give a VERY good feeling of sinister pleasure when you at last kill him. And to pour salt on the wound, Astrid was arranged to be MARRIED to Lekain.
Fire Emblem Jugdral has Manfroy. He used every hero and villain as a pawn in Gen 1, plus killing every single one of his pawns indirectly. Also he got another Magnifecent Bastard, Alvis, to unknowingly marry his sister and brought back a dark god, thus getting him under his thumb.
Ganondorf is one of the few video game villains that is shown to consistently win. In nearly every game in the main franchise, Link has to clean up the mess he made well after the fact. And since he holds the Triforce of Power, he is effectively immortal; you can defeat him, but he won't die. Even with the Master Sword, he can only be "sealed". Of course, since the first game is chronologically one of the last games in the timeline where Ganondorf triumphed over the Hero of Time, it's possible to hypothesize his power had waned significantly over time and multiple defeats. Thus far, there's only been one timeline with a game implying he's been Killed Off for Real, which is pretty impressive stuff.
Yuga from A Link Between Worlds definitely qualifies. Considering Ganon is explicitly named in the prologue, that's an impressive feat. To be specific, this guy hijacksGanon. Not to mention, he is the only character in the series to possess more than one piece of the Triforce at a time bar Link himself.BAD. ASS.
General Shepherd from Modern Warfare 2. The guy decieved and used everyone for his own goals for glory and power. He sett up all the events in the game by first using both Allen and Makarov by somehow conspiring with the latter, his own enemy, to use the former in a plot that would provoke Russia to declear war on USA, and with him as the leader of the latter nation, it would bring him the glory he wants as he would defeat the enemy troops and win the war. When Captain Price re-enter the scene and, the Crazy Awesome guy as he is, make some things that weren't part of Shepherd's plan, Shepherd is still able to use them as well for his own advantage. Even when he dies he still gets his victory, as he'll be remembered as a war hero, and Soap and Price as terrorists for killing him.
Though she may not have managed to impress fans sufficiently, Amelissan from Baldur's Gate II: Throne of Bhaal would qualify based on her actions. She had almost everyone convinced that she was a kind of activist dedicated to helping the weaker of the mortal children of Bhaal, the dead god of murder, while she was secretly herding them all in one place to be killed. She had the most powerful five convinced they could become demigods by destroying their lesser siblings in order to resurrect Bhaal, while her intention was to destroy them as well. And she had the dead god himself convinced she was going to resurrect him from the essences of his children, when she intended to use the power to become a god herself. When she encountered the Player Character, she had them kill all the other powerful Bhaalspawn while making sure they stil couldn't save the weaker ones in the city where she had led them. The reason why she's not really hailed as a Magnificent Bastard may be that she wasn't very convincing to the player from the start... and that she was a bit of a psycho when she showed her true colours.
Bhaal himself qualifies as well. After foreseeing his death in the Time of Troubles, he began a remarkably elaborate fail safe plan by walking the mortal realm before the Time and knocking up the women of nearly every race and culture, giving birth to thousands, if not millions of mortal children that each carried a sliver of his divine essence. After his death, he and his high priestess began orchestrating the mass slaughter of those children so that their essences could return to Bhaal, eventually causing him to be reborn stronger than ever. And he may very well have succeeded, if it wasn't for that fact that his high priestess decided she wanted his power for herself.
Azura from The Elder Scrolls orchaestrated the Nerevarine Prophecy that drives Morrowind's plot in order to punish the Tribunal for a centuries-old insult. Not only does it go just as planned, but it ultimately leads to the world being saved three times.
King Helseth is also one of these. One amazing example of this is in an in-game book detailing how he roots out one of the many spies in his midst: 
Viking: Battle for Asgard: Freya raises one warrior from the dead with the promise of being given another chance to gain entry to Valhalla. What does she get in return? She gets one dead god and an entire world at her fingertips, essentially. Too bad Skarin doesn't look kindly on her not living up to her promise and killing her and the entire pantheon.
System Shock has SHODAN. After her ethical restraints were removed on Citadel Station, she copiously gloats about how superior she is to all organic life, especially human beings, while not even trying to hide her ambition to destroy the planet with Citadel Station's mining beam. This trope was taken up even further in the second game. when you find out that she posed as Dr. Polito to establish trust, and threateningly orders you to dispose of her creations, The Many, which serves as a common foe for you and SHODAN. She also recruited Dr. Marie Delecroix for the same task, promising to aid her all the way, but instead abandons her and leaves her for dead. She leaves you for dead, too, after you destroy The Many, and then you fight and "kill" her... only to realize she's possessing Rebecca Siddons! SHODAN defines malevolence, cruelty, and insanity.
Grand Theft Auto: San Andreas has Mike Toreno, an undercover government agent who fakes his own death at your hands while infiltrating a drug cartel, only to show up out of nowhere with your brother's life over your head so he can get you to do some of his dirty work for him. Between having eyes and ears everywhere he needs or knows you will be, and talking you out of shooting him without even flinching, he definitely qualifies for the trope.
Relius Clover is best known for his development and refining of machinery, but he also has a knack for leading others along a road of his own design, hence his nickname "the Mad Puppeteer". He tends to have a number of flexible backup plans for many a situation and is capable of improvisation to boot, so he can walk away with at least something learned for the future. His crowning achievement is That Which is Inherited, wherein he conned Sector Seven into providing him research and materials for the mechanized weapon known as "Fluctus Redactum: Ignis", up to and including manipulating Kokonoe into evoking a larval Black Beast and compressing it with "Infinite Gravity" into a core for Ignis to use. Granted, he isn't perfect - Kokonoe catches on to what he goaded her into doing and cut him down with Nirvana while he was defenseless - but he has proven that he isn't easily shaken when his plans go awry... or much of anything, for that matter.
Yuuki Terumi has plenty of manipulations to his name - much of the conflict in the plot can be chalked up to his hand, ranging from effing with Ragna's childhood to anchor himself to this world to placing Noel Vermillion as the secretary to psychotic Jin Kisaragi as a means to mentally wear down both her and Tsubaki to goading Trinity into lifting Nine's geas on him before proceeding to backstab them both - this last one is the whopper that left him running free in the first place. His moving pieces into place is due to his being able to witness events in multiple timelines as a side effect of being Takamagahara's pawn, which he used in tandom with the magical prowess of the aptly-named Phantom (who is all but outright stated to be an enthralled Nine) to lobotomize them at the end of Continuum Shift.
However, at the same time, Terumi's mental screws had long since come loose, and the varying outcomes of the continuum shift actually allowed that to show. While being able to see every possibility of the continuum shift is a distinct advantage, Extend's Slight Hope reveals that it is a crutch - he is utterly screwed against a tactical equal unless he eliminates them immediately, and sometimes even Relius cannot save his plans. All attempts at manipulating Makoto Nanaya without the aforementioned crutch have invariably ended in failure, with one attempt utterly destroying his schemes outright and another nearly doing so until he happened upon her by chance, and Chronophantasma shows no signs of Terumi slowing her down. If the iterations of Chronophantasma - namely, one where Taokaka's scuffle with Noel sends her away from a NOL restraining squad - are any indication, that crack in his alleged omniscience may be widening...
Interestingly, Rachel Alucard counts as a rare heroic example, even leaning more towards being a Guile Heroine in Continuum Shift than in Calamity Trigger. To be fair enough, she, like Slayer in Guilty Gear, is one of the only characters in the franchise who knows what the hell is going on. She shows herself to be quite a skilled Chessmaster as well as a remarkable Manipulative Bitch, especially as shown in her Continuum Shift gag ending. Not only does she use the Nox Nyctores Tsukiyomi to defend Kagutsuchi from Take-Mikazuchi in Calamity Trigger's True Ending, she also proves to be by far one of the most powerful characters in the BlazBlue universe, capable of keeping up with even Terumi himself.
Izanami the Goddess of Death and the true antagonist of the series she like her Persona counterpart used Terumi and Relius as her pawns and later abandons them to their fates.Plus she brainwashes Ragna in joining her and took Phantom who is Nine with her to create her ideal world of death.
This also means that throughout the entire game, he was outthinking THE REAPERS, machines that are millions, possibly billions, of years old and have committed galactic genocide hundreds of times over.
In between the second and third games, he shows his Magnificent Bastardy by manipulating and eliminating the Shadow Broker, Liara, and Aria, all of whom are Magnificent Bastards themselves. The only reason that the final parts of his plan didn't go forward (which involved the deaths of Aria and Liara, not just the destruction of their organizations) was because Shepard intervened.
Less conventionally but no less awesomely, Morinth. She's a Chaotic Evil and quite insane serial killer who kills her victims through sexual intercourse (other methods are implied, but that appears to be her favorite), but seeing her in-game, it's quite easy to see how she charms her victims with or without biotics, making her one of the most frightening characters in the trilogy (and that's counting the Reapers). If she joins your crew, she not only pretends to be her mother in full view of the crew, but even has the quads to proposition Shepard for sex, even though both of them know how that'll turn out. The sad part is you can agree to it. Guess what happens?
Sovereign. The guy pulls off a string of plans: Keepers not responding? Indoctrinate the rachni and use them to take over the citadel. Council defeats rachni with krogan? Use the years of galactic stability to indoctrinate the geth, turn the Council's best operative against them, cause tension within by destroying human colonies, and then launch a new Pearl Harbor. Amateurs manipulate people. Sovereign manipulates entire species.
The Reapers are an entire species of Magnificent Bastards. Everything they do reeks of Dangerously Genre Savvy, all their plans put in place with a devious and sinister Batman Gambit, masters of Xanatos Speed Chess, and both directly and indirectly manipulate everything from behind the scenes. You practically HAVE to be this to successfully commit systematic genocide against all advanced organic life every 50,000 years for AT LEAST the past billion years.
Aria T'Loak doesn't get much opportunity to show it on-screen, but she is implied to be this in Mass Effect 2, since she's made the most Wretched Hive in the galaxy have only one rule: "Don't fuck with Aria", and successfully juggled all the mercenaries, pirates and killers for centuries in order to stay on top, while still being something of a Noble Demon. It is also implied that she's Aleena, the asari who managed to fight Urdnot Wrex to a draw, and that she deliberately changed her identity to avoid having to kill him. She then came to Omega as a dancer, until she ended up soundly defeating the previous ruler of Omega (also a Krogan), and then kept him alive as an advisor/trophy, and when he is threatened she can (depending on the player) save his life without looking weak by seeming to care.
Mass Effect 3 proves that she really is this; even though she gets forced off Omega by the aforementioned Illusive Man, she moves to the Citadel to bide her time (apparently with very little loss of power and authority), and when she has trouble with immigration she simply calls the asari councillor, one of the most powerful people in the galaxy, and tells her to sort it out. She also fully recognises that it would be flat-out idiotic to focus solely on her own goals until the Reapers are defeated (thereby averting the We Are Struggling Together that virtually everyone else, including the Illusive Man, is falling into,) and presents Shepard with various ways to gain the loyalty of three dangerous mercenary groups, (catering to all moral alignments in the process,) and also gets in some excellent Deadpan Snarkery in the process.
In the Omega DLC, Aria enlists Shepard to help retake the eponymous station from Cerberus. Although her original plan is refreshingly direct ("I think I'm going to employ violence"), her opening gambit is a well-executed False Flag Operation involving a genuine Cerberus cruiser her troops captured, which allows her to decapitate and overwhelm Cerberus's superior space forces. Then, when the occupation force reveals they've improved the stations' guns, she casually tells Shepard that she planned for this, installed enough element-zero explosives on her cruiser to turn it into a giant disruptor bomb, and sets it on a suicide course into the station's shields. She and Shepard escape in a boarding pod and land in Omega. Then it transpires that, due to higher-than-anticipated casualties, she needs ground troops. So she heads over to the base of the Talon mercenary gang, who she has just learned have been fighting off Cerberus, only to discover another bombshell: the Talons' leader is her ex-lover Nyreen Kandros, who has turned them into a highly principled resistance army. With one speech, she manages to rally Omega's repressed citizens and the Talons, and nabs Nyreen in the bargain by playing on the turian's sense of duty towards those same common citizens. Unfortunately, it's all almost for nothing — Nyreen dies entirely by accident, causing Aria to snap, go on a killing spree, and blunder into a Cerberus stasis trap. Fortunately for Aria, she chose the very best commando in the galaxy to back her up, and Shepard rolls over the rest of the occupation in his/her own inimitable style.
And let's face it, Shepard (particularly with a high renegade rating). Not only will potentially do ANYTHING to achieve his/her goal, (s)he can manipulate baddies into surrendering, and even talk them into killing themselves, and in Mass Effect 2 you can cooperate with Cerberus and still screw them over at every possible turn. And if you resist the (undeniably irresistible) urge to punch reporters, you can have a thoroughly good PR as well.
Wild ARMs 2 has what may or may not count as a heroic example. Irving creates both the heroes' organization and the villains in order to set them against one another, with the end result that the victor will have united the world and prepared them for a greater threat: a living alternate universe that eats other universes. He then successfully sacrifices both his sister and himself in order to give that universe a living body for the heroes to kill. His grand scheme saved the world from an unfathomable threat at the cost of his own life, but it still left a terrible taste in the protagonists' mouth.
In Alpha Protocol, Mike Thorton himself can become one of these if you play your cards right, build up your contacts, and manipulate your opponents correctly, effectively allowing Mike to Take Over the World.
First is Augustus, who effortlessly manipulated Felgorn to murder the Emperor so that Spoiled Brat Helga could take over, then let her run the Empire into the ground so that when he covertly assasinated her, everyone would rejoice and appoint him Emperor. And when Felgorn finally wises up and turns on him, Augustus allows him to kill him, stating in his dying breath that he was content and that, in a way, he had already won.
Second is Big Bad Castor. He first uses his cunning and charm to rise through the ranks and become the Commander of the Kingdom's armies, secretly manipulating his own king for his own purposes. Oh, and he pretended to be the toady to Grandmaster Ortas, who thought he was the one in control, when in reality Castor was always aware of his genocide plot, and was simply waiting for the right moment to expose and kill him, further raising his status.
Finally, there is King Valkiris, who manages to be possibly the biggest Magnificent Bastard despite being a backstory character. This is a man who, through sheer cunning and charisma alone, managed to effectively rewrite history to his benefit.
Naoya of Devil Survivor makes a huge plan that manipulates a demonic cult, angels, demons, his cousin/brother and his friends, and the entirety of Tokyo. Why? To make his cousin/brother take a potshot at GOD and start a war.
Valkyrie Profile: Covenant Of The Plume has chessmasters in Mistress hel and her personal hound, garm AKA ailyth, who instruments the entire artolian war and events leading up to and around it to provide plenty of chances for wyl to gain sin for the plume, all to make him her personal chewtoy.
The first Dawn of War campaign has Sindri Myr. Causing an entire planet to descend into slaughter and madness was merely a sideshow to his manipulations of Bale, Gabriel and Isador, constantly leading them exactly where he wanted them, none of them believing themselves to not be in complete control, all for the purpose of using an Artifact of Doom to ascend himself to Daemon Prince status and unleash a Sealed Evil in a Can, both of which were successes. He was defeated in the end, but as Daemon Princes are immortal he is probably still around somewhere, being magnificent.
By doing the Wild Card questline in Fallout: New Vegas you can install yourself as the new ruler of the Mojave Wasteland while stringing along both the Legion and NCR up until the last minute.
Robert Edwin House: Cheated out of his inheritance by his step-brother, he nevertheless manages to go to MIT, become a major innovator in the field of robotics and is a self-made billionaire by the time he's in his thirties. He also buys out several other companies, including that of his erstwhile sibling.
After predicting the date of an impending nuclear apocalypse, he concocts a plan to save the city of Las Vegas and assure the future of humanity. As it happens was only off by twenty hours, and in spite of missing the Platinum Chip that would have further optimized his countermeasures, the system he put in place manages to ward off most of the nuclear missiles heading for the city.
About 200 years later, he detects NCR scouts in the Mojave, which prompts him to take control of area and rebuild the ruins into New Vegas. While still nowhere near powerful enough to resist a hostile takeover, Mr. House manages to negotiate a treaty that allowed the city to remain independent in exchange for giving the NCR a military base as well as most of the power from Hoover Dam. With the Fiends cropping up in North Vegas and the Legion camping out in the southeast across the Colorado River, the NCR is effectively pigeonholed into defending New Vegas and respecting the terms of the treaty. And to add to the insult, it's their citizens that are powering the city's economy through gambling.
Yukari Yakumo of Touhou sleeps most of the time and rarely, if ever, involves herself in anything, but that's because she doesn't need to. The entirety of Gensoukyou is under her metaphorical thumb, nothing occurs of which she isn't aware, and whenever she says "jump" everyone else says "how high?". She organised the first invasion of the moon, as well as its failure, solely to teach youkai a lesson about expansionism, and founded Gensoukyou centuries before its purpose as a refuge of magic would be necessary. With her level of power she could easily solve any problem instantly, but it is so much more fun to get others to do it for her.
The NEXUS entity from Warzone2100, originally a top scientist known as Dr Alan Reed, he was the one who created the synaptic link technology, enabling a person to upload their consciousness into cyber space. Then the US Government pulled his funding due to a lack of progress, what does Reed do? It's implied he uploaded his consciousness into cyber space and created the NEXUS Intruder program, which resulted in his gaining control of the USA's entire nuclear defense network and firing off all their nukes, then ensuring they were unable to defend against retaliatory strikes and resulted in the collapse. When the Project rose up he ordered the New Paradigm and The Collective to attack them, watching as the former were easily crushed and then fired off a nuke at Beta Base while the latter attacked, allowing him to destroy all three quickly while having access to all the technology they found. When The Project took the fight to him he seemed to have a counter for everything they threw at them. Stop the nukes from firing and he sets them to blow up with you in the area, go to librate another Project base and you discover he already assimilated it and used it to trap you. You gain access to your own missiles and he sends laser satelites and waves upon waves of enemies at you. The only thing that caused NEXUS' defeat was the the laser satelites going unstable and buying time for you to destroy them.
Iris Zeppelin of RosenkreuzStilette. For starters, she acts like a kind, innocent girl, which won her the trust and love of her fellow RKS members, just to hide her own evil intentions, and is quite fond of pulling Wounded Gazelle Gambits when other people are able to see through her facade to the evil within her. She orchestrated a rebellion launched by RKS against the Holy Empire strictly For the Evulz, and had Karl imprisoned by her father because He Knows Too Much. Since she is a reincarnation of Rosenkreuz, blessed with absolute power and unparalelled brains, she arranged for her father to launch the coup in order to protect her from the Empire, who knew what she was and feared her so much that they wanted her dead (of course, he didn't know that she started the coup for her enterainment). She also orchestrated for her entertainment Spiritia doing the "Swiper, No Swiping!" deal with everyone, pitting her colleagues against her ideals, and amused herself watching Tia give it her all, leading her to think of her as a Worthy Opponent. She even arranged to have Grolla's deceased grandfather and mentor, Raimund Seyfarth, brought Back from the Dead by her father as The Grim Reaper. All this went according to her plan to become a god herself thanks to her power, intelligence, and talents she got from being reincarnated from Rosenkreuz himself. Did we mention that she orchestrated making it look like she was kidnapped by her brainwashed dragon slave Talos to have Tia pick up her pendant so she could observe her every move, too? And lastly, to be fair and to top it all off, she's quite theatrical with everything she does, too!
And let's not forget the fact that she has some rather nice Evil Plans too. Some of them mainly revolve around making other people like Zorne and Grolla suffer, and you can always expect her to win as soon as she pulls off a You Have Outlived Your Usefulness on her daddy and lays bare her plan to give her adoptive sister every minute of her suffering, and as soon as Grolla finds herself both so infuriated and deeply hurt that she blames Iris' daddy for disrupting Raimund's peaceful slumber, vows to kill him, and EVEN hits him with a This Is Unforgivable. Heck, you can always expect EVERYTHING to go everything according to her plans unless someone like Freudia or Grolla intervenes. You know what this means? She's become quite the Draco in Leather Pants that you Love to Hate! Truly such a great example of a Magnificent Bastard that Light Yagami, Sosuke Aizen, and even Byakuran should be proud of her.
And even better. She even has a backup strategy in the form of destroying HER OWN palace after being bested by Tia (and Grolla) by invoking her tiara's power and activating the palace's self-destruct mechanism, and, just like Dr. Wily, whom she's an Expy of herself, escapes not long after beginning the destruction of her own palace. And it catches both off guard. She did this both #1: in an attempt to crush Tia with the palace itself not long after she told her about The Power of Friendship helping her punch her out and told her to give it up (after which of course Iris said that she let her guard down), and #2: to prevent herself from being killed by the hands of such a "mere commoner" as Grolla (at least Grolla caught this attack and escaped to avoid falling to her death). Of course, she didn't know that Talos saved Tia in a Crowning Moment of Heartwarming. And, knowing that there's a sequel in the form of Freudenstachel, she might return in said game to pull off more of her Magnificent Bastard pranks.
Oh yes, definitely. Iris indeed returns in Freudenstachel and orchestrates the Schwarzkreuz's kidnapping of Tia in the beginning of the game to have her all Brainwashed and Crazy. Her manipulation of the entire organization into attacking both RKS and the Holy Empire lands her even further into magnificent bitchery.
And then there's Iris' Dragon, Eifer Skute, who also manages to be another one. Eifer played a role in helping to kidnap Tia in the beginning of the game and manipulated her own "colleagues" together with Iris, keeping her true intentions a secret from them all. Even if she was just another of Iris' pawns, acting as an ally to her own "colleagues" before revealing herself to be her confidant also very much qualifies for magnificent bitchery.
Dragon Fable's Sepulchure. He spoke truly that the dragon hatched from its egg from the White Dragon Box that was supposed to save the world would end up helping him to destroy it once he made him his undead pet. He even has a move where, whenever the hero switches items, he automatically retaliates with the words "I saw that." Then he raises his attack power and randomly uses one of his attacks.
It's also possible for Drakath to count as one in AdventureQuest Worlds as well, in a complete departure from his whiny, stubborn, and incompetent self in Dragon Fable. He managed to outsmart his own former master Sepulchure in covering his armor with signs of Chaorruption upon attacking him and then ripping out his heart and crushing it, destroying him in a massive explosion. He spares King Alteon to let him watch his age of Chaos begin in Lore, and orchestrated for his 13 Lords of Chaos to summon their respective Chaos Beasts in each of their respective locations in order to light one of the different archways on the portal behind him and therefore destroy one of the seals placed on it. After the current Chaos Lord is defeated by the hero, Drakath, pleased that the Chaos Lord served his purpose well due to the hero accidentally falling victim to a Nice Job Breaking It, Hero either through blunder or by being tricked, chooses the next Chaos Lord to replace the current one, no longer having a need for him/her/it. He even thinks of the hero as a Worthy Opponent, too, and helps him/her defeat Ledgermayne because it disobeyed him, proving that Magnificent Bastards have standards, so he can let him/her fulfill more roles in his plans. Yup. He may have threatened to swallow all of Lore with Chaos, but Drakath is one of the kindest Magnificent Bastards of them all, willing to punish Ledgy for being The Starscream to him as well as an Omnicidal Maniac.
Ledgermayne outsmarted Drakath once when it disobeyed him. Because it was self-aware living magic that not only was immune to known weapons and magic, but could also control other people's magic. That's saying something.
Kitsune, the fourth Lord of Chaos, also qualifies. After becoming so courtesy of Drakath and being convinced by him to release the O-dokuro from the rift of time, he used his Chaos powers to place Emperor Daisho under a spell and stole the Hanzamune Dragon Koi Blade after waiting for the hero to defeat Ryoku. He had Neko Matta have the hero run around killing Skello Kitties and Nopperabo as a trick to buy Kitsune just enough time to use the sword to summon the O-dokuro from its prison. And what makes Kitsune even more magnificent is his affinity for illusion, trickery and lies, and the fact that, unlike the Shredder, whom he's an Expy of, he is rarely cruel. Of course, he didn't count on the hero retrieving the sword from the O-dokuro's head and using it to close the rift pouring a waterfall of Yokai out of it, which led him to see him/her as more of a problem than he first thought.
The Master (a.k.a. Exos) in the Skyguard storyline also seems to have shades of this. He arranged for his spies to infiltrate the Skyguard Academy and for his Dragon, the Dreamweaver, to fool all the Skyguard by taking on many different forms to deceive them. However, over the course of said storyline, he started showing signs of panic and worry, and eventually fell short once Invidia (the Dreamweaver in disguise) betrayed him, reducing him from a possible Magnificent Bastard to just a pathetic, pitiful Smug Snake.
In the Doomwood saga, after he was killed by the Dragon Fablehero, Artix, and Vayle in Dragon Fable, Noxus learned from his mistakes and evolved into a Magnificent Bastard, guiding Sally to the Necropolis with his ghostly voice to train her as the supreme Necromantress of the Tower of Necromancy. After she completed her training, she repaid him by resurrecting him as a lich. Eventually afterwards, Noxus found an ancient evil that, with Sally's help, he used to create the Nigh UnvulnerablePaladin-Slaying Vordred. Vordred turning almost all of the paladins except Artix undead was just as Noxus planned.
And even better. While the hero was fighting his/her way through the Temple of Doomwood, Noxus left his office at the Necropolis for Shadowfall, after which he/she, Cysero, and Beleen stormed it only to find out that he wasn't there. Noxus and Vordred attacked Shadowfall to Gravelyn's rage, and upon finding out that she was Sepulchure's kid, he not only turned all her undead minions to his side, he also decided to use her as bait to lure the hero and Artix into a trap. Thus, setting off the scene for the Shadowfall War. And what's even better? He even makes Gravelyn wear her slave bikini as Fanservice to AdventureQuest Worlds fans. And of course, had he known that Gravelyn had an undead minion of her very own who could not be affected by his magic, Noxus would've been the one who won.
Krellenos, the ninth Lord of Chaos, is rather sneaky and manipulative. He's always one step ahead of all the other Trolls as well as the Horcs plus he operates smoothly in his plans without anybody noticing.
Desoloth truly earns his reputation as one as well. He masterminded X'Dir tricking the hero into releasing him from the Dragongate with the Dracoscintilla he / she collected by killing the four Prime Dragons in the Dragonplane, and after the plan succeeded, Desoloth declared that the hero was to be his first meal in 800 years. However, he was actually rewarding him / her with a test of skill and power because he was curious how powerful the residents of Lore had become over the years he was imprisoned. And he's even nice enough to leave a shade of himself in the Dragonplane so the hero can fight it whenever he / she wants. And best of all, Desoloth earns bonus points for being a dragon because, as all dragon fans say, "dragons are awesome."
The Mysterious Stranger/Dhows/Erebus is a master of this trope, the only reason you manage to beat him is because of his ego getting the better of him and letting the player give him a name, a very Meaningful Name.
Guilty Gear brings us the mysterious Ano Otoko, also known as "That Man" and the Gearmaker. He shows a great deal of power as Sol and Baiken unsuccessfully attempt to strike him hown in their respective endings in XX. In Anji's ending he invites him to his side and later in XX Accent Core Plus hires him to track down and punish his Co-Dragon I-No for all the trouble she's stirring up. He knows that Sol's ability to use Dragon Install could very well one day help to save mankind from a possible future threat. Not only that, his intentions also seem whole-hearted, as he appears to be full of remorse for everything that's happened during the Crusades.
Meta Knight from Kirby. He, to be fair enough, is one of the only characters to know what the hell is going on, is quite manipulative, and manages to be a Worthy Opponent, which appeals to the fans and makes him a Draco in Leather Pants. In Kirby Squeak Squad, one of the only games where he doesn't offer Kirby a sword (the other being Kirby's Epic Yarn), he knew the secret of the chest stolen by the Squeaks and fought Kirby to prevent something terrible from happening (which of course turned out to be Dark Nebula being released). He's so awesome and badass that he even gets his own variation of the victory tune that the Kirby characters get in Super Smash Bros.. Also manages to be That One Boss.
In the anime, Meta Knight is shown to be even more manipulative and even lean more towards being a Guile Hero. He's willing to help Kirby in certain circumstances, but mostly wants Kirby to learn on his own. He even points out what he's often been manipulating Kirby himself into doing: "In order to mature, Kirby will have to be pushed to his limits. Only then will he learn the true mastery of his powers and therefore turn the tides of the battle."
And how can one possibly forget about Marx, from Kirby Super Star? He got the sun and moon to fight. He manipulated Kirby into going into space to summon Nova just so he could have his wish to Take Over the World granted. It was all according to his plan. Now, if he had counted on Kirby flying into Nova to stop it by destroying its nucleus, he would have succeeded. And interestingly enough, as evidenced by using Nova's parts to revive himself, Marx also Came Back Strong.
And more recently: Magolor, who tricks Kirby, Meta Knight, Dedede, and Bandana Waddle Dee to beat a four-headed dragon for him so that he can steal its crown for himself. He appeared to be a friendly alien at first, but actually wanted to use the crown to rule the universe.
The Practical incarnation from Planescape: Torment is this in spades. He devises traps that only his immortal future-selves can surmount, sets up a multi-lifetime plan to stop the Ascended One, and does a royal number on Dak'kon by essentially brainwashing him and manipulating his religious views with the fabricated circle, just for access to his sword. Also, what he does to Deionarra just to get a spy in the Fortress of Regrets.
Also, Ravel, even if she loses out anyway. Kinda.
Trilby from the Chzo Mythos series counts as this, as summed up in the final scene of the short story spin off by game creator Yahtzee, 'Trilby and the Ghost' when he tricks a ghost into stepping into a chalk circle that will exorcise him: "'You're a devious bastard, Trilby.' Claire said. 'I guess that's why they called me.'" Also seen in the games, especially when he tricks the other characters at the end of 5 Days a Stranger into thinking that he was burnt to death in a fire to avoid being captured by police.
The player character in Tropico 4. In particular, there's The Plan of the Isla Desconida mission, where the player character, in order to become recognised as a legitimate head of state, begins developing an unsettled island, petitions an undisclosed European country to give the island colonial status, then leads a socialist revolution against his own colonialist regime. The Soviet agent and Penultimo are both pretty confused by the end.
While he does show signs of smugness about his own incredible power and has a habit of saying several forms of "This Cannot Be!" many times when he's defeated, Count Dracula of Castlevania fame definitely counts as a classic example of a Magnificent Bastard. His plans almost always involve being resurrected himself at certain times, and he's willing to have anyone - even his own minions - sacrificed to do so himself. If he's not at full power yet, his plans to become resurrected work every time. And since he has his As Long as There Is Evil gig, this makes perfect sense. He's Faux Affably Evil and learns from past mistakes. Definitely magnificently bastardly indeed.
And as if everything he does in order to be resurrected and/or become at full power didn't make him magnificent enough, what better way to make him even more magnificent would there be without any mention of Mathias Cronqvist from Castlevania: Lament of Innocence? He and his close friend Death [[spoiler:used Leon Belmont to defeat the vampire lord Walter Bernhard just so he could get the three stones for himself and use them to become the immortal king of the night himself.
Death counts as well. He's a very Affably EvilChessmaster of a Grim Reaper who's so faithful to his master that he's willing to make any sacrifice - even sacrifice himself - to revive his lord, and carefully orchestrates many plans involving those sacrifices to do just that. What an intelligent dick.
And, surprisingly, she finds herself outsmarted by Dmitrii Blinov, who turned out to have feigned defeat earlier just so he could obtain the same ability as Soma Cruz. Upon realizing this, she takes back what she said to Soma and leaves for the Abyss with him... only to be sacrificed by him later. If it weren't for Dmitrii succumbing to the Power of Dominance and creating in his place the Final Boss Menace, Celia's efforts wouldn't have been for naught.
Skantarios from the "I Am Skantarios" after action report. The player role plays a ruthless conqueror so well that you rather wonder about him.
The online game epicMafia is full of this on a daily basis. For example, in http://www.epicmafia.com/game/873944 the player "QQ Whore" fakes that he has a report on the last mafia member forcing them to admit to their guilt, before explaining that he was in fact lying through his teeth.
Hades from Kid Icarus: Uprising can be considered this. For one, he tricked the humans into killing each other to increase his Underworld army troops, taking their souls to make more soldiers. He took so many souls that he was able to resurrect Medusa and made a copy of her just to use as a distraction for Pit and Palutena while his troops continued to attack the humans to gain more souls for his army. Hades was also so powerful that he managed to outright destroy BOTH sacred treasures when battling Pit. If not for Medusa interfering in their final confrontation, there's no doubt that Hades would've killed Pit for sure.
Jericho Swain of League of Legends. Sure he may look like a hobbling cripple with a cane, but this guy is in the League of Legends and therefore automatically Bad Ass, and has done such magnificent things as somehow convincing his superiors to TAKE A DEMOTION SO HE COULD COMMAND THEM. An entire plotline in lore which involved the creation of Dominion, at least one new champion, Damacia and Noxus working together, and several Journals of Justice turned out to be all part of Swain's plan to take over Noxus, which succeeded before anyone truly realized, and once they did, they simply said that's fair. He got a new skin out of it too, Tyrant Swain, which makes him look like he should be the Final Boss, that is if League Of Legends were that kind of game.
The titular character Zero, from the series Zero Escape, deserves a mention: We're talking about a character who is able to access the morphogenetic fields, allowing her to send her consciousness forward and back in time, and thus predict events and actually change history:
In Nine Hours, Nine Persons, Nine Doors, it's revealed that Zero is actually Akane "June" Kurashiki. She sets up the events of the story, joining the game as a player, along with her brother, and orchestrating the death of numerous persons (and traumatising many others) in order to survive the traumatic event which unlocked her powers in the first place, 9 years ago, and get back at the people who did this to her at the same time. Please note that she didn't kill anyone directly: she offered them an other way to atone for their crimes, but since she knew Ace wouldn't, she manipulated him so he ends up killing his fellow collaborators (the man was more interested in saving his own hide than anything else). During all the game, the player believes he is playing as Junpei, while in fact it's revealed that he's possessed by Zero's consciousness from 9 years ago. As for Akane, all her actions during the game are actually an act, allowing her to manipulate the events of the game from the inside easily.
In Virtue's Last Reward, it's revealed that it's in fact the same Zero, Akane, who is responsible for the events of the game. She orchestrated the game's events specifically in order to train Sigma and Phi, so that they can access the morphogenetic fields, and then use them to change the past and stop the disaster which happened in 2029 which led to the death of nearly 6 billion humans. She joins once again the game, but is killed in many timelines, something she is fully aware of, as part of her Thanatos Gambit. In the course of the game, she injects all 9 participants (including Quark, a young and innocent boy, and excluding Luna, since that one isn't human to begin with) with a mortal disease which slows down their time perception and which would ultimately lead them to commit suicide, kidnaps 3 of them back in 2028 and cryogenizes them for a period of 45 years, lures one in the game (since he's a key part of her Thanatos Gambit), lures an other one and his boy into participating as well (since Tenmyouji is in fact Junpei, and he was lured in under the pretence that he would meet Akane again), and even mess with the timing of the bombs so said timing would be adjusted to their already slown-down time perception. In the timeline she isn't killed, she disguises herself as K, and in the end she pushes Sigma to activate his powers by threatening to kill Phi in front of him. In the secret ending, Junpei, after finally meeting her, gives up on her, saying basically that the Akane he knew and who he looked for for years was gone. Only time will say if her plans succeed in the next Zero Escape game.
The Prime Evils of Diablo became one in the game's backstory: they deliberately lost a war with their underlings so that they could be exiled to the human world.
Diablo in Diablo III: masterminding his own resurrection so that he'd absorb all the lesser evils into himself.....and the Player Character helped him accomplish this for 2nd and 3rd acts.
Robert de Sable from Assassin's Creed I. The guy not only just controlled the Knight Templars, but also the Crusaders and the Saracens as well, and right below the noses of both King Richard and Saladin, and neither of them knowing it. And when Altair had assassinated several of his men, he uses the murders for his own advantage by nearly convincing King Richard to ally with Saladin in order to crush the Assassin Order, since his men were both Crusaders and Saracens. And he also tricked Altair in a trap while he did it, by disgusing one of his followers as him when Altair was hunting him, and only because Altair is an One-Man Army did that trap failed.
Haytham Kenway from Assassin's Creed III fits in as well. Just like Robert de Sable, he had the Loyalists and the Patriots in his pockets influencing decisions throughout the American Revolution wherever he saw fit. Haytham had plans running all over Colonial America, from stealing tribal lands to an assassination attempt on George Washington and several other leaders of the Continental Congress. The Templars under his leadership nearly wiped out the Colonial Assassins, and even after his death he established a permanent Templar presence in America for the years to come. The best part was he started the Revolutionary War allying himself with the British, but they turned out to be mere pawns, he intended to remove them from the Colonies and establish America as an independent nation under the Templars.. His only downfall was that he cared deeply for his son Connor, and intended to make peace with him but he put his Templar ideals before his own son. Not to mention of the fact that he fights like a complete badass.
Tyber Zann in the Forces of CorruptionExpansion Pack to Star Wars: Empire at War. What else do you expect from Grand Admiral Thrawn's most capable student at the academy, before Thrawn had him expelled for stealing weapons. The expansion describes how Zann carves out a criminal empire (the Zann Consorcium) that rivals that of Jabba the Hutt and manipulates Thrawn himself into executing Xizor, the leader of a rival syndicate, for him. While Thrawn is able to outwit Zann at least once by bribing a mercenary in Zann's employ, Zann comes out on top in that battle, forcing Thrawn to flee. At the end of the campaign, Zann plays the Empire and the Rebellion against one another while he moves in to capture the most powerful ship in the Empire's arsenal (as far as he knows at the time), turning its powerful weapons against both fleets.
For the record, the part where Thrawn is able to outwit Zann by bribing Bossk into giving him Zann's holocron was also planned by Zann. Zann planted a homing beacon on the artifact to lead him to his true goal - the Imperial Archives. Thrawn firmly believed that the fleet he left to defeat Zann would easily win. Zann surprised him by bring out his newest Aggressor-class Star Destroyers and obliterating the force Thrawn left.
Giovanni from Pokémon tends to be portrayed like this in the adaptations.
Dr. Eggman can sometimes be depicted like this. Some examples include him controlling the Time Eater with the help of his past self with the goal of undoing his previous defeats in Sonic Generations, tricking Sonic (while in his super form) to let his guard down long enough to extract the energy of the Chaos Emeralds from him and turn him into a werehog in Sonic Unleashed, and faking his death to power up his ultimate weapon while having Sonic get rid of the Deadly Six for him and put his plan back in motion in Sonic Lost World.
Shadow the Hedgehog was actually quite an impressive one in Sonic Adventure 2. He manipulated Eggman into thinking he was working for him so that he could get all the Chaos Emeralds in order to activate the Colony Drop, and even knew about Rouge's attempt to grab the Emeralds herself. In fact, the only reason he didn't succeed was that, with Amy's intervention, he decided to not go through with the plan after all.