"Ah, how shall I do it? Ooh, I know. I'll turn him into a flea, a harmless little flea, and then I'll put that flea in a box, and then I'll put that box inside of another box, and then I'll mail that box to myself, and when it arrives, ahahaha... I'LL SMASH IT WITH A HAMMER! It's brilliant, brilliant, brilliant, I tell you! Genius, I say! (BAM) ...Or, to save on postage, I'll just poison him withthis!"
Take Over the World: Of course! This is the most popular villainous scheme of all. The scale of conquest can vary depending on the setting — some warlords are content to settle with conquering a kingdom or nation, while Science Fiction overlords will go for nothing less than galactic, universal or even multidimensional domination.
The Evils of Free Will is a popular means to this end: by robbing everyone of their free will, they will have no choice but to serve their rightful ruler!
Destroy The World: Why take over the world when you can blow it up? Like Take Over the World, the scale of destruction also varies depending on the setting — some villains are content with merely destroying a city or kingdom (particularly if they feel the city or kingdom has somehow wronged them — see Vengeance Is Mine), while Science FictionOmnicidal Maniacs may well wish nothing less than to destroy the entire universe or multiverse.
Cause The Apocalypse: Not so much destroying the world or humanity as really screwing up civilization; though the former two may be involved in the bargain.
Vengeance Is Mine!: You know that guy that wronged you in the past? It doesn't matter how petty or misplaced your grievance is, it's payback time! Time to kill the bastard, or make his life a living hell!
Get Rich Quick: If you're already rich, get richer. Any scheme is fair game in the pursuit of the profit margin, be it theft, blackmail, or auctioning the world off to hungry demons. Unfortunately, this lust for wealth falls prey to poor planning.
Frieza wanted to become immortal so that his position as the most powerful being of the universe would be secure for all time. After Goku kicks his ass, his goal changes to destroying the Earth for revenge on him.
Cell wanted to destroy the Earth and kill Goku because he was programmed to, but possibly For the Evulz as well.
Etc.
The villains of Sailor Moon have their own plans but they all want to collect Macguffins for power, like energy or heart crystals etc and used the Monster of the Week format to get them.
Inukami!: Two (maybe three) major villains with plans ranging from "erase the nudity taboo so I can walk naked in public without shame" to "push people beyond the Despair Event Horizon because I am a Emotion Eater".
Kekkaishi The first Big Bad wanted to take over Katasumori to restore his Ill Girl princess back to life.
Cowboy Bebop has a number of villains but the recurring one, Vicious, wants to take over the Red Dragon Syndicate and settle a long-time score with Spike Spiegel.
Cardcaptor Sakura: Invoked by Eriol. He pretends to be a shadowy villain with a devious agenda to give Sakura opportunities to transform the Clow Cards.
Wedding Peach: The Big Bad Reindevila and her devil minions are afarid of angels attacking themAllergic to Love so they try to ruin relationships The source of angel power and find the Saint Something Four, which amplifies love waves and according to a prophecy, would destroy their world.
Astro Boy: Skunk has them when he appears; usually either revenge on Astro or making money. Tenma's larger scale plan is a world where robots rule the world and are ruled by Astro himself.
Magical Girl Lyrical Nanoha: A strange example as it there isn't one until Fate shows up. Yuuno just needed help recovering artifacts scattered by an actident. Eventually its revealed that Precia wanted the jewel seeds to revive her real daughter and 'go back to way things used to be.
Sister Princess: For a given value of evilAkio's plan to seperate Wataru from his sister and Promise Island is the only thing resembling an overarching plot in the series and forms the climax.
Grey: Big Mama, AKA Toy, believes humanity as a whole wants to self-destruct so it created the Trooper wars to help it reach that goal faster.
Comic Books
All of the events within the first 12 issues of Red Robin were planned by Ra's Al Ghul, who was testing Tim Drake's worthiness as a potential father to his next heir apparent. Which ended up an Aborted Arc when the universe rebooted before it could be finished.
Fanfiction
Ultimate Spider Woman 'Change With The Light' did this with Jack O'Lantern, Spider-Woman's Arch-Enemy as well. Jack immediately minimizes most of the risk to himself by using Corrupt Corporate Executive Phillip Watson as his mind-controlled dupe and making it look like Phillip is the one pulling the strings. Jack is giving Phillip instructions on what to say and do, and makes sure to delete all his correspondence with Phillip so it can't be traced back to him. The plan works out just as he'd hoped — the resulting Mob War decimates two of New York City's crime syndicates, allows him to begin implementing his Legion of Doom plan to set up a new supervillain crime organization, Phillip is blamed for the whole thing and Jack gets off scot-free, and he manages to give Spider-Woman a No-Holds-Barred Beatdown as the final delicious twist.
Time Lords and Terror: The Carrionites wish to extend the empire into Esquaria by using the S'Müz.
Dr. No's plan was to topple American rockets from his island base as part of a mission from SPECTRE, probably with a hostile foreign power as a client.
Kronsteen and Rosa Klebb in From Russia With Love wanted to steal a cryptographic device from the Soviets and sell it back to them, as well as take revenge on Bond for killing Dr. No. This was also a SPECTRE mission.
Goldfinger's scheme was to nuke Fort Knox to devalue American gold and increase the value of his own.
Emilio Largo's plan in Thunderball was to steal two nuclear missiles and try to get ransom from the U.S. by threatening to launch them. This, too, was a mission from SPECTRE.
Blofeld's plan in You Only Live Twice was to start World War III by destroying American and Russian spacecraft and framing the other. Again, SPECTRE had been hired to do this by a hostile foreign power.
Blofeld's plan in On Her Majesty's Secret Service involves hypnotising a group of 12 unwitting divas and arming them with a virus that causes infertility in the plant and animal life of his choosing, unless the world meets his demands of immunity from past crimes and to be recognised as a Count.
Blofeld's plan in Diamonds Are Forever is to use stolen diamonds to build a Kill Sat and hold the world hostage.
Kananga/Mr. Big from Live and Let Die wanted to corner the heroin market.
Scaramanga, The Man with the Golden Gun, wanted to corner the market on solar power during the '73-'74 energy crisis. Bit of an Excuse Plot- the real meat of the story is that Scaramanga has abused his girlfriend one too many times and she has duped Bond into going after him by making it look like Scaramanga has taken a contract on his life.
Stromberg from The Spy Who Loved Me wanted to start World War III by hijacking nuclear submarines and launching them at New York and Moscow respectively, as in You Only Live Twice framing both countries a perpetrators of the others plan. He will then build and rule an underwater city as a paradise for the survivors to rebuild civilization. Yes, he is insane.
The Plan of Hugo Drax of Moonraker was the annihilation of the human race in order to repopulate the world with his own "ideal" specimens. Given that the original villain of Moonraker was a Nazi, this shouldn't come as much of a surprise.
Kristatos in For Your Eyes Only wants to recover a MacGuffin for the KGB, and to manipulate Bond into assassinating his rival as a bonus.
Renegade Russian General Orlov in Octopussy wanted to detonate a nuclear warhead on an American base (making it seem like an American accident), forcing the US to pull out of Europe and leaving it vulnerable to Soviet conquest. He is in a Big Bad Duumvirate with Diabolical Mastermind Kamal Khan who is getting paid for it, and hopes to kill his boss / partner in crime in the process and take over her organization afterwards.
Max Zorin's ultimate plan in A View to a Kill is to detonate explosives along the Hayward and San Andreas Faults, causing them to flood. The other major bomb was set to destroy a "geological lock" that's in place to prevent the two faults from moving, causing a double earthquake that would destroy Silicon Valley, leaving his microchip company with a monopoly.
The evil plan of Big Bad Duumvirate General Koskov and Brad Whitaker in The Living Daylights is to get ludicrously rich using the profits from a large shipment of opium paid for using diamonds and to repay the loan from the Russkies they took and are a bit late in returning, as well as pitting the British against the KGB chief who is on to them by framing him for murdering British agents.
Sanchez's scheme in Licence To Kill involves cocaine hidden in gasoline sold to Asian drug dealers, conducted via a televangelist, revolutionizing the drug smuggling business. He's also bought Stinger missiles from the Contras and is threatening to use them on American airliners if the DEA didn't back off. The story, however, is more about Bond's Roaring Rampage of Revenge for what Sanchez and his people did to Felix Leiter and his new wife.
Alec Trevelyan of GoldenEye sought revenge against the British government for betraying his family, who were Lienz Cossacks sent back to Stalin, by detonating the titular Kill Sat over London. Furthermore, he planned to steal billions of pounds from the Bank of England — as well as all sorts of data like credit ratings, land registers and criminal records — and the records of the transactions will be zapped, leaving him very rich and leaving the British — and indeed, the world — economy in shambles.
Elliot Carver of Tomorrow Never Dies wanted to start a war between the West and China to increase the ratings of his media empire, and then to murder the Chinese government so his ally in the military could take over, who would give him exclusive media access (China being the only country in the world that refused him broadcast rights after he gained the ability to reach the entire world with his new satellite system).
The World Is Not Enough has Elektra King and Renard scheming to raise petroleum prices by triggering a nuclear meltdown in the waters of Istanbul, destroying every oil pipeline except for hers and giving her a monopoly on Europe's oil.
Die Another Day's Big Bad, Gustav Graves, takes a page from Blofeld's book from Diamonds Are Forever and uses a diamond-powered Kill Sat that runs on solar energy. He sought to use it to help North Korea take over the South, as well as Japan and presumably elsewhere (he is actually a corrupt North Korean colonel Faking the Dead and in disguise as a wealthy Corrupt Corporate Executive).
Casino Royale involves one bad guy, criminal banker Le Chiffre, who short-sells successful companies and engineers terrorist attacks in order to sink their stock values and turn a profit. The other bad guys are his superiors and clients who are pissed because he is doing this with their funds and behind their back. Bond screws up Le Chiffre's plan by foiling a terrorist attack and Le Chiffre has to hold and win a multi-million dollar poker tournament to pay his clients back. Bond is there to win it to force Le Chiffre to sell out his clients and superiors to MI 6 in return for sanctuary before the other villains track him down and kill him.
Quantum Of Solace involves Dominic Greene wanting to hold the revolutionary government-to-be of Bolivia over a barrel by controlling the majority of the water and not oil through a system of planned underground demolitions.
Sky Fall is a little underwhelming. The villain's evil plan, as complex as it is in execution, is just a personal vendetta against M with no grander ambition.
And while we're at it, Never Say Never Again is a rehash of Thunderball with SPECTRE hijacking nuclear weapons and holding the world hostage; Casino Royale 1967 spoof is much the same as above, except Le Chiffre is (as in the novel) working for SMERSH instead of terrorists and his double-dealings (which, again like the novel, has nothing to do with Bond) are a side-plot to SMERSH's master plan, which involves murdering spies all over the world (like the Real Life SMERSH, a Soviet counter-intelligence agency) and to fill the world with a biological agent at the behest of its Diabolical Mastermind Doctor Noah aka Jimmy Bond, the real James Bond's nephew, a.k.a. Woody Allen. The agent will kill all men over 4'6" (his height) and make all women beautiful; in other words leaving him as the "big man" who gets all the girls.
Dr. Leopold from MST3K-film The Blood Waters Of Dr Z has one of these on a huge chart with each step illustrated, and which he crosses off as he completes them.
The Kagenos' true goal in RoboGeisha is to drop an atomic bomb into Mt. Fuji, which they believe will destroy Japan so that they can rebuild it in their own image.
Season of the Witch: The villain is a demon who seeks the only book with the knowledge of how to banish it back to Hell in order to destroy it and the entire movie is the heroes helping them find it.
Austin Powers International Man Of Mystery parodies this trope. Dr.Evil explains various evil plans only for his Number Two to point that they already have happened. At last he throws up his hands and says, "Let's just do what we always do: hijack some nuclear weapons and hold the world hostage."
Captain America: The First Avenger: It's WWII and the Nazi's Deep Science Division has splintered into their own group and are trying to take over the world.
The Avengers: Loki's back and this time he wants to take over the Earth with help from the Chitauri.
Mystery Men Casanova Frankenstein plans to use the Psycho-De-Fraculator on the city, which will fry their brains. No one knows why he wants to do this, but then again, he did spend the last thirty years in a nut house.
The Book of Eli: Carnegie searches for The Bible so he can use it to expand his "kingdom" with 'good news' rather than mooks with guns.
Happy Gilmore: An odd example in that the plot's initial conflict, Mrs. Gilmore lossing her house, is not the real villain's plan. Instead, that would be Shooter's attempts to kick Happy off the Pro Tour for stealing his thunder.
Literature
Voldemort in Harry Potter wants to make a perfect society (one ruled by wizards, pure-blooded wizards, loyal only to him), rule it (with much pain and torture and fear), and become immortal. In fact, the immortality is probably the most important to him.
The especially ironic part of this is that while he vaunts the so-called purity of blood among wizards, he is himself not a pure-blood wizard - he is a half-blood, as his father was a Muggle (non-wizard) whom his witch mother tricked into eloping with her with a love potion because she loved him (which he did not reciprocate).
In Brandon Sanderson's Mistborn, we find out at the end of book 2 that The entire plot of the first and second books were engineered by Ruin in order to get Vin to release him from the Well of Ascension. Also, the search for the Lord Rulers' Atium stockpile which took up a good part of book three was yet another gambit by Ruin. Although to be fair, the Lord Ruler and the Terris prophets had planned for this eventuality.
No matter how minor the case in The Dresden Files, eventually it will turn out to have at least one of these behind it.
Going Postal: Big Bad Reacher Gilt is an even bigger con artist than our Boxed Crook protagonist Moist von Lipwig. Gilt wants to corner the communications market by keeping the post office closed, so he can make as much money as possible off the Grand Trunk semaphore line before it goes bankrupt (then he can buy it up under an assumed name and repeat the cycle).
Evil Overlord Gothon conquers one kingdom after another in order to enforce a uniform peace. He also wants to capture Ben so he can save his wife.
he's actually being manipulated by Kazebar. He told Gothon that Ben's soul could revive her so he could get his hands on the boy and steal his latent power to travel to other worlds and become a god.
Man in Shadow has a different agenda. All that is revealed in this book is that he's working for people with larger ambitions.
Light And Dark The Awakening Of The Mage Knight: Shadows want to wipe out life on earth. They're the reason for the trouble. On a more personal level: Syndil wants to find the Bonded containing Danny's father's soul so he can find the Black Bonded. He manipulates Danny into providing him with clues to which one it is. It's implied that his plan is expanded to include measuring the Mageknight's power.
Protector of the Small is unusual in that the cause of the conflict, the Scanran king, is a non-entity and even his Evil Genius is only present in the final book. Until then Kel only has to bother with a classmate's petty jealousy.
Likewise for Daughter of the Lioness but this time because the royal family of the Cooper Isles is Royally Screwed Up and tends to off each other.
Haroun And The Sea Of Stories: Khattam-Shud seeks to poison the Sea of Stories because he can't rule the fictional worlds inside them.
The Pendragon Adventure: Saint Dune's end goal is killing the seventy thousand survivors of the ninth book's climax and destroying all the free will in Halla, as well as Halla itself. This would allow him to become the new god of the Dark Solara and new Halla.
Song at Dawn: Inverted. It is The Hero Dragonetz who is stirring things up with his paper mill and The Church is trying to stop him. Some of them are business minded but others believe he truly is doing evil because his mill is made from Islamic (i.e. infidel) technology. Other, lesser, villainous plans are as follows:
Raymond de Toulouse has the classic take over place X goal but this is a minor plot thread and is treated by everyone like 'business as usual'. Everyone is trying to take over everyone else.
Alis' pranks are driven by eny of Estela.
Young Wizards: The Lone Power has a "Gift" (i.e. death) and wants everyone to have it though the reasons why vary based on the specific aspect the wizards are dealing with. In some cases the Power is a proud inventor, in others It's genuinely malicious, and in others It thinks It's being helpful.
Adventure Hunters: In a classic case of turning a trope on its head, so does this book do to this trope. The evil king, Jerrod, is more of a Jerkass king only interested in holding control of both banks of a river that divides his kingdom from his neighbor, Ryvas. It is Ryvas, The Good King, who engages in devious scheming to awaken an Artifact of Doom but only because Jerrod is infringing on his land and economically strangling his people.
Forever Gate: Someone is doing something to the gols that is causing them to dengenerate. Since the gols run everything, this puts the integrity of the entire human civilization at risk. It's the reason Hoodwink's daughter gets involved with the Users and thus the reason Hoodwink started this plot.
Howl's Moving Castle: The Witch of the Waste wants to claim Howl's heart, metaphorically. This is why she chases him and curses a rival (Sophie) into old age. The demon contracted to her, Miss.Angorian, wants to claim his heart, literally. This is why she arranges a series of events that will allow her to get inside the castle and grab Calicifer.
Live Action TV
Star Trek: Deep Space Nine: What do you think Weyoun and all his Cardassian underlings talk about in all those staff meetings? Yamak sauce recipes?
The whole episode 3: Every case Sherlock has to solve ends up having been orchestrated by Moriarty, looking for a fun challenge. It's implied that he, as a consulting criminal, has been arranging a vast array of crimes all over the place.Subverted in that the whole thing was to distract Sherlock from the plans. Revealed that the plans were a McGuffin, and double-subverted, when Moriarty tosses them away.
The entirety of episodes 4 and 6 were also extremely convoluted plans orchestrated by Moriarty as 'levels' in The Game he's playing with Sherlock.
In Mesogog's case from Power Rangers Dino Thunder, he was motivated by racism, believing dinosaur DNA to be superior, and attempted to return the planet to its prehistoric roots by turning humans into mutant dinosaurs with him as the supreme ruler.
The Tempest A rare heroic version; the entire play is Prospero's God Game to end his exile from Milan. 'Heroic' because all he wants is to get his home back and teach his evil brother a lesson. No one gets hurt, not even the evil brother, and almost all of them go back to Milan as more or less friends.
Video Games
Raphael from the Soul Series has some of the most ridiculously insane plans ever devised, all for his adopted daughter. In Soul Calibur 2 he planned to destroy the country that he fled from by giving its nobles the Soul Edge on the basis that they would tear the country apart in a demonically-dueled civil war so that the world would..somehow.. be safer for his adopted daughter Amy. In Soul Calibur 3, on discovering that he and Amy had been accidentally turned into basically vampires, he decided to turn the entire world into creatures like them so Amy wouldn't feel left out. Amy may constitute a pretty drastic subversion of a Morality Pet.
Shining Force III: The plot to abduct Emperor Domaric in the third game is a rare villain-on-villain Evil Plan, perpetrated by Domaric himself. When he hears that one of his sons is plotting to have him killed, blame it on the breakaway republic of Aspinia, and use the resulting war to seize the throne and conquer the rest of the continent, Domaric sends his own agents to infiltrate his son's conspiracy and allows himself to be kidnapped. Then, when the empire's armies are geared up to invade, Domaric has his mole "free" him, takes control of said army, and marches on Aspinia - just as he's wanted ever since the country seceded 20 years before. He even corners his son's partner in the whole plan, to force him to use an ancient superweapon to break down Aspinia's walls for him.
Tales Of Symphonia: Mithros wishes to revive his sister and end discrimination, and to do that he splits a world in two and makes them fight over Mana while his evil army antagonizes the dying one. The first part is Unwitting Pawn and the rest of the game is the heroes unraveling the plan and how to foil it.
Tales Of The Abyss: The Big Bad and his minions are more upfront about their goal of ending The Score but unraveling the details and creating a counter measure still drives the bulk of the plot
In the Baldur's Gate series, Bhaal the Lord of Murder sired the the Bhaalspawn in order to revive himself. They would kill each other until none remained, at which point his essence that was scattered among them would have accumulated, and his chosen follower, Amelyssan, would have performed rituals that would have brought him back. Neither Amelyssan nor the last Bhaalspawn (the protagonist) complied to these plans, however.
Saints Row 2: Dan Vogel's plann is to strike a deal with the winner of the gang war and get credit for cleaning up Stilwater. The Boss nuked that dream nicely.
In Mass Effect 3, the Illusive Man attempts a massive one: to take control of the Reapers themselves and use their overwhelming power to bring complete human dominance. As brilliant as he was, it doesn't work and he ends up indoctrinated for his efforts.
The fifth Wild Arms game has Volsung plan to reformat the planet so it will stop rejecting veruni and making them sick. Unforunately this process will kill every human on the planet.
The first game, Melody of Elemia, has three villains acting more like convenient allies than a single group which means there are three of these.
Mir wants to wipe out humanity to create a world just for reyvateils because she believes that Humans Are Bastards.
Bourd wants to continue the kind of research that's based on the 'Reyvateils are replacable dolls' idea and believes Mir to be its greatest fruit.
Bishop Falss, AKA Kyle Clancy wants to ressurrect Mir and take over Platina as the first step to taking over the world and returning it to the prosperity of the first age.
The second game, Melody of Metafalica is a touch more complicated. Basically, the world is in trouble because of Shurelia shutting down the tower to stop Mir from killing all the humans under her jursidiction and there are many groups with their own ideas on what to do about it.
A third Well-Intentioned Extremist group wants to spread I.P.D to create a powerbase for Clouche to draw on and sing Metafalica and create brand new land.
The Nod Prophet Kane is an uncontested master of these, and in Command & Conquer 3: Tiberium Wars and Kane's Wrath pulls of an absolutely staggering one. Short version: the entire Third Tiberium War was orchestrated start-to-finish to bring the Scrin aliens to Earth and allow Kane to steal their technology.
In Mega Man Zero 4, Dr. Weil's plan is to destroy Area Zero and the restistance with it.
Super Smash Bros. Brawl, anyone? The Subspace Emissary? The gambit is here enacted by none other than King Dedede. Yes, they are being serious. As the game's website revealed that was in a cancelled scene, Dedede uncovers the truth about Big Bad Tabuu, who has taken command of a replicable army, the villain/occasional ally of his enemies (the Super Mario brothers) Bowser, the pure villain Ganondorf, the gun-for-hire of Wario, and has even successfully taken control of the local godlike entity, Master Hand. Oh, and he's got bombs that drag chunks of reality into a separate dimension being produced by the dozens through a race of robotic beings being held hostage through secondary villain Ganondorf. So, what does Dedede do? He creates timed badges that, after Tabuu uses his Off Waves to kill off all the other fighters, revive whoever they've been stuck to. If the others defeat this enemy, that's all fine and dandy. If they fail? Ol' Dedede's hidden backup come out of nowhere to take down Tabuu while he's essentially helpless, busy creating a new world in Subspace. But how is it that none of the villains notice what he's up to? Simple - Dedede acts like he's claiming them as prizes. This kind of greed is common place in Dedede's usual acts of villainy. Not only is the man setting off an Evil Plan, but he's utilizing Obfuscating Stupidity in order to ensure his true intentions aren't suspected. Good lord, all of that from easily one of Nintendo's most infamous bumblers.
As of 2nd Original Generations, Euzeth Gozzo has been confirmed to be the mastermind of a spanning multiple parallel universes to assimilate all destructive technology he can in order to surpass the creators of the original Cross Gate Paradigm System and become powerful enough to destroy Keisar Ephes permanently.
Broken Saints has a whole big complicated scheme. The short version? Lear Dunham wants to bring down the corrupt power systems of the world and end the suffering they cause. To do so, he plans to use various high-tech gadgetry to blast a Mind Raping "God signal" across the entire planet. Major world leaders and military honchos implanted with a certain chip — a chip they thought was supposed to protect them while the blast took care of their enemies — would find that in actuality the chip enhances the signal, and all implanted with the chip will die horrific deaths, and surrounding un-chipped populations would be hit with massive psychic trauma. The rest of humanity would receive the signal but would not die; instead they would hear the ominous voices, see the giant "eye of God" in the sky, and feel the signal-stimulated fear in their hearts, and submit themselves to the angry God. Those few whose brains are less prone to the signal's power would be drawn to Lear's Evil Tower of Ominousness, where he would make them his apostles, helping him rebuild the world. Oh, and in order to broadcast the "emotion" element of the signal, he uses his own daughter, an empath born and bred to fulfill precisely this function.
He later teams up with Gamma, another AI, and the Freelancer Wyoming in an evil plan to subvert the aliens' religion from within, thereby defeating the aliens and taking control of their entire species. And possibly conquering the universe with their new army.
The Necromancer of the Whateley Universe has one, but it still hasn't been revealed, because he's still at the Grand Theft MacGuffin stage of the plot.
He still had a massive plan in play just in "Ayla and the Birthday Brawl" where he found out Ayla was having a birthday party in Boston. He spun it into a plan to: break his minions out of the inescapable superjail outside Boston; find out which of his other minions was The Mole; steal yet another MacGuffin; create a hostage situation to get yet another MacGuffin; take out the SWAT teams that would get sent to that hostage situation; get Fey under Mind Control or worse; and also kill a bunch of Ayla's friends, just to send a message to someone who had pissed him off. He pulled off most of it.
The Daily Victim plays this for laughs when an employee of an obscure gaming mag plots to get his people into a con. When they get there, he asks the guy at the door to give them their passes. Which he does. The narrator, expecting a refusal, has already set his non-defined, incomprehensible plan into motion. The installment finishes with him desperately trying to stop his associates before they start their part of the scheme.
General Mistlethwakey from EHUD Prelude To Apocalypse has his 'Plan', an elaborate gambit to... um... well, his goals haven't been made clear yet, but he did sic a pack of supersoldiers on the former president, and then spin the resulting public panic to get his underling made president... so there's something there.
Both Lord Doom and Doctor Simian, from the Global Guardians PBEM Universe, are masters of this craft. At one point, both Criminal Masterminds used this trope against each other, with the heroes as pawns. To say it was messy was to say the Pacific Ocean is a little damp.
HeretiCorp: 1) create an army of invincible alien clones to conquer the world, 2) locate Oasis by making the trigger for her homicidal rages the symbol for a national fast food chain.
Chilus: release a swarm of mind-eating insects to bring about "the end of the world through bugs" as prophecied.
Dr. Steve: brainwash his adoptive daughter so she can "go on a date with a lesbian and then tell all." Okay, they can't all be winners.
In Dead Of Summer, Doug Fetterman has one. It involves making an evil clone of Panther to replace the real one, getting rid of the real Panther, downloading crucial information from KILROY, reformatting KILROY, killing Dr. Light, getting the fake Panther to elect him leader of the Protomen, and destroying all who stand in his way.And if that fails, blow them up using the reformatted KILROY as a Time Bomb.
Joel Calley from Concession has manipulated much of the overarching plot seemingly to destroy his older brother for taking their father's company and leaving and killing his twin sister whose vengeful ghost is the reason Joel can't let it go.
In Fans!!, this trope backfires. Feddyg captures Hilda and replaces her with a duplicate controlled by him, ultimately sending it to kill Rikk; Hilda, instead, causes it (apparently her) to shoot itself in front of him, who's already anxious about the new program. Might have thought that one out better.
In S.S.D.D the Oracle does these out of boredom. For example it would create a superweapon so powerful that the world would have no choice but to destroy it simply to watch its efforts in accomplishing such a goal.
Boris and Natasha go through many Evil Plans on Rocky and Bullwinkle, such as a sinister plot for giant, robotic mice from the Moon to eat through American TV antennas so that entertainment-starved Americans will flee the country, leaving it ripe for conquest. Boris is, of course, the Big Cheese.
Cobra Commander from G.I. Joe once wasted a huge amount of resources stealing equipment to build a giant laser... so he could carve his face in the moon. Destro was not impressed.
Another attempt by Cobra Commander was to use a love potion to allow The Baroness to seduce a ship magnate, only to have a fight break out between Cobra and G.I. Joe over the chemical, only to have the potion stolen by a crab. At least this time Destro found the whole silly fiasco hilarious.
Endlessly lampshaded and over and over again by the various Card Carrying Villains of Kim Possible. In fact, while tutoring another villain, Shego explains how it's the single most important part of being a villain.
The Robot Devil in an episode of Futurama: "My ridiculously circuitous plan is one-quarter complete!"
Played every which way with Phineas and Ferb 's Dr. Doofenshmirtz, whose main goal is to "TAKE OVER THE TRI-STATE AREA!". He's not above the occasional revenge sideplot or a little mind control, but ultimately, he wants to rule. The alternate-universe Doofenshmirtz in the "Across the 2nd Dimension" movie has alt-Doof trying to take over the multiverse's... tri-state area. Some things never change.
The villain in the first season of Wakfu looked for fuel for his MacGuffin, so he can undo a past wrong. In the process, he nearly destroys an entire race, justified by "it will all be undone when I'm successful." In the end, though, it seemed that his MacGuffin isn't very 'fuel-efficient'.
Regardless of the villain, the plan usually boiled down to 'kill Batfink'
In The World's Greatest Super Friends, Mxyzptlk tries a scheme in a deliberate Whole Plot Reference to The Wonderful Wizard of Oz with Superman, Aquaman, and Wonder Woman. The imp makes the big mistake of letting his victims get back together after their individual adventures, compare notes and realize their experiences were suspiciously similar. As a result, the heroes deduce the common element of the scheme, sabotage it, and then sucker Mxy with some Briar Patching into banishing himself.
In the Code Monkeys episode "E.T.", Mr. Larrity buys the rights to make a game based off Steven Spielberg's movie E.T. the Extra-Terrestrial. In an obvious nod to the horrid real-life E.T. game for the Atari 2600, Dave goes to a strip club instead of the movie, and just makes up stuff for the game, which ends up sucking. As it turns out, Mr. Larrity had pinned the making of the E.T. game on a rival company, Bellecovision, and had also been paid a substantial amount of money by George Lucas to discredit Spielberg by making a crappy licensed game based off his movie.
Santa Claus in the Phineas And Ferb Christmas special inverts this trope by incorporating Doofenschmirtz's evil scheme to fulfill the odd Christmas wishes of Phineas, Baljeet, Buford, Candace, and Doofenschmirtz. This also just happens to restore the faith in children of a curmudgeonly elf.
In Ed Edd N Eddy, Jimmy, the effeminate kid in the cul-de-sac, successfully engineers one of these in the episode "If It Smells Like An Ed". He frames the Eds for ruining his Friendship Day celebrations, leaves false clues for them to follow, uses Rolf as his Unwitting Pawn and strikes a deal with the Kanker Sisters, climaxing with the Eds trapped in a shed left to choose their fate: getting beat up by the kids or raped by the Kankers? They get both. And why did this happen? Because Eddy gave Jimmy a wedgie.
Mildew will stop at nothing to banish dragons from Berk. He thinks they're Always Chaotic Evil because he spent his life fighting them. In truth, every episode further proves they're actually Always Lawful Good.
Later episodes establish Alvin The Treacherous with a different goal; he wants to conscript 'the Dragon Conquerer' (i.e. Hiccup) so he'll have his own Dragon Riders
God The Devil And Bob:The Devil wants to tempt Bob into sin so he'll go to hell, just to spite God.
