Agent Valentine: You have broken every arms embargo written. There is enough evidence here to put you away for consecutive life sentences. I don't think you appreciate the seriousness of your situation. Yuri Orlov: My family has disowned me. My wife and son have left me. My brother is dead. Trust me, I fully appreciate the seriousness of my situation. But I promise, I won't spend a single second in court. Agent Valentine:[after Yuri is proven right] I would tell you to go to Hell, but I think you're already there.
The villain always loses, right? Actually... no. Sometimes the villain surprises us all and is victorious, even if only in the short-term. However, victory comes with a price. Both they and the audience may well ask if it wasworth it. Often this takes one of two forms: either it has taken so much effort (and such underhanded methods) to win that it has left the good guys as the moral victors with a better legacy, or in order to accomplish their goal the villain has had to sacrifice what they cared for most and/or made them likeable and/or relatable-to for the audience.
So while their efforts might have paid off, to answer the earlier question of whether it was worth it: frequently it is not.
See also The Bad Guy Wins, for where the villain doesn't suffer from this. This sort of plot may be found in a villain's Start of Darkness, back when the villain was either a hero or a much lesser villain, and first turned to true villainy, bringing victory... but at a cost. On the other hand, really top notch villains may win without sacrificing everything, only to find that Victory Is Boring. A Meaningless Villain Victory is when the villain wins but a sudden unforeseen event renders their victory hollow and their efforts for naught. Being Evil Sucks also counts if the villain in question have a Heel Realization about the choices he made.
Needless to say, this is an Ending Trope, so beware the spoilers!
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Anime and Manga
Harry McDowell in the anime version of the game franchise Gungrave first just wanted enough power to live his life freely and protect the people important to him. With time, he succeeds in rising to the top of Millennion and making it more powerful than the law itself, but only by losing sight of his original goals and betraying almost everyone he cares about. He's driven to kill both Brandon, his best friend whom he relied on in all his life (leading to some spectacular Villainous Breakdowns), the fatherly prior head of the organization and his wife, Brandon's sweetheart. Twenty years later, though, he's finally able to face Brandon and come to terms with his life.
Conversely, in the game's continuity, he shows no remorse for killing Brandon/Grave (Harry in the game's storyline is depicted as little more than a complete prick). Either way he still wanted Mika, the innocent daughter of Grave's former love interest dead. Harry even had Big Daddy used as a guinea pig and mutated him into an acid flame-spewing monstrosity, just to see what kind of effects Necro-Rise/S.E.E.D. would have on him and has no qualms about siccing Big Daddy on Grave as the Final Boss of the game. As a result, Harry dies, Grave lives, and moves on with his "life" with Mika.
Seen in Hell Girl. Yes, your contract with Enma Ai gives you what you want: to punish someone who's slighted you big time. However, by sending that person to Hell, you've condemned yourself as well, since when your life comes to an end, you will join them in Hell. See the mark on your chest? It'll remind you of the Deal with the Devil you made.
In HellsingThe Major succeeds in defeating Alucard, even though Integrakills him in the end. Also, London ultimately rebuilds and life continues on like normal. And just like the last time he was soundly beaten, Alucard is never truly out of the game; he comes back eventually.
Happens twice in JoJo's Bizarre Adventure, Cars, the main villain of Part 2, gets what he wants which is to become the ultimate lifeform, which lives forever and can adapt to any environment or situation, but ends up flung into space, where he will live forever, but slowly go insane from the boredom. Enrico Pucci in Part 6 kills most of the heroes and obtains his vision of "heaven", if only for a moment... but then gets killed by a mere child, and the world then gets the Reset Button; and he's no longer in the universe, having never been born.
Although it may depend somewhat on your interpretation, SEELE's plan doesn't seem to have turned out the way they intended by the end of Neon Genesis Evangelion.
Chairman Keel seemed quite pleased with the outcome. Presumably they are among the people who can't "imagine themselves in their own hearts", so no free resurrection card for them, but that's apparently what they wanted.
Shinji, arguably, fits this trope better. In both endings this is what he wanted. In both endings, he got better, but after getting what he wanted... well, Alexander the Great might have wept over no more worlds to conquer, but thanks to Shinji there's no longer a world.
Gendo certainly didn't get what he wanted. Rei rejected him in favor of Shinji, and it's implied that he is not reunited with Yui in the psuedo-afterlife that is Third Impact, since as (what appears to be) Yui/Unit 01's response is literally biting his head off.
In Saint Beast, having defeated two justified rebellions from the angels, Zeus is sick of war and decides to retire and go into a long sleep.
One Piece: The Paramount War. Oh sure, the Marines may have killed Ace and Whitebeard, but now they have a pirate who has two of the most powerful devil fruit powers in the world and absolutely no self control to go with it, an entirely new age of piracy, a bunch of former prisoners of Impel Down running around free, and the WORST generation of pirates in the Eleven Supernovas, all while being severely weakened due to the war with the loss of three major assets (Sengoku, Garp, Aokiji), and lots of other, smaller, assets, leaving them utterly unable to deal with the problems caused by the war. Fitting consequences for a stupidly short-sighted plan.
In the Emperor Doom Graphic Novel, Dr. Doom succeeds in conquering the world by brainwashing everyone. By and large he's a fairly benevolent monarch and does much to solve many of the world's problems. Unfortunately, he's so bored out of his mind that when the one unaffected hero manages to break the spell on a few others, he lets the rebellion win. He'd rather be a conqueror than a Desk Jockey.
This is a running theme with Dr. Doom; every time he manages to take control of a nation/planet, he'll spruce the place up very nicely and run it better than most governments ever manage, but will ultimately get bored of running it. Doom enjoys the challenge of taking over a nation and solving problems, not the mundane managerial work of keeping national status quo.
The exception is in Doom 2099. He conquers the United States, and actually intends to keep power, so he can fix the entire world. It doesn't end well for him, the country, or most of the heroes.
In Triumph and Torment, this is how Doom saves his mother.
The end of the Civil War plays with this: Iron Man's reputation has essentially become mud because of his support of the SHRA, and it's only further compounded by Captain America's death.
"It was the right thing to do! And I was willing to get in bed with people we despised to get this done. And I knew the world favors the underdog and I would be the bad guy."
Archie Comics' Sonic the Hedgehog had an early, non-canon Yet Another Christmas Carol where Robotnik is taken to see the future. Robotnik has finally defeated the Freedom Fighters, but he has rendered himself the last man alive in doing so, turning Mobius into a barren wasteland. However, Robotnik doesn't grasp this, and fails to learn his lesson.
While not technically a villain, the Finance Smurf from The Smurfs comic book story of the same name gains the entire village after all his fellow Smurfs, including Papa Smurf, have left it behind along with all their money...only for himself to be left without anybody to share his new-found good fortune with, making him very sad and lonely. This makes Finance Smurf come to his senses and go out to find the Smurfs to tell them he's giving them back everything and abolishing the money system.
Played with in The Batman Adventures's final issue with "Fear Itself": Joe Chill ended up in jail on an unrelated charge after shooting Thomas and Martha Wayne, meaning that the policenote and Batman overlooked him. By the time he finds out just who he shot — and just who the boy that he'd spared that night was — said boy's become an "untouchable millionaire" long out of Chill's reach, and Chill's is depicted as seeming to be living relatively scot-freenote and in fact, he would have been... except for his constantly hallucinating the adult Bruce Wayne's face wherever he goes, spending every day day in mortal fear that someday Bruce Wayne will remember his face and finally finger him to the cops. Not only do Batman and a GCPD detective both not recognize his face, Batman actually mistakenly believing Chill to be a henchman of Killer Croc'snote ironically, Chill has no idea who Croc is, but finding out his real name and his alias doesn't ring a bell either, meaning that Joe Chill was in a hell entirely of his own making.
There is a Final Fantasy VIIAU story in which Sephiroth achieves his goal of godhood, only to "rule" over a dead, unpopulated landscape, doomed to wander forever through a barren world alone and abandoned by Jenova. It climaxes with him falling to his knees, screaming in agony and irretrievable insanity.
On a similar note, there is a Star Wars fanfic where Anakin wins the duel with Obi-Wan on Mustafar, but Padme dies before Palpatine's ship arrives. Anakin promptly turns on Palpatine and kills him, and spends some time ruling the galaxy, searching for a way to bring Padme and the twins Back from the Dead, slowly going crazier all the while. Naturally, it's a massive case of Came Back Wrong when he finally does try to bring Padme and the twins back, and Anakin responds by wreaking havoc on the galaxy in his fury. In the end, he returns to Mustafar, where he spends eternity sitting on a throne in the middle of the hellish wasteland, surrounded only by the bodies of Obi-Wan and Palpatine (and maybe Padme), and talking to the bodies as though they were still alive.
Care to tell what the name of this fanfic is?
When All Your Dreams Come True, an Avatar: The Last Airbender fic, explores what would have happened if Prince Zuko had actually managed to capture Team Avatar. The results are nightmarish, with Sokka publicly lynched and his corpse put on display in a museum, Katara forced to spend the rest of her life fighting in a gladiator arena in order to bloody virgin troops, and Aang is bodily mutilated to the point where he can't threaten anyone, to the point where the last we hear of him is him having gone insane to the point where he begs his guards to let him out to feel the sun on his skin one last time. And the worst part for Zuko, aside from the guilt of seeing that happen? No one back home believes he actually captured the Avatar. They think Iroh did and then gave the credit to his incompetent nephew. The fic ends with Zuko escaping into a fantasy life where he made friends with Team Avatar, while outside in the real world the Fire Nation wins the war.
Discussed in the Daria fanfic "God Save The Esteem." Helen (who owns her own private firm in this universe) is in an intense debate with the school's attorney, Jim Vitale, about a case involving Daria. Helen points out that if the case goes to court the victory could go either way, and given how much bigger his firm is than hers, even a slim victory will look embarrassing for his side. After a moment of thought, he agrees to settle.
In Necessary To Win, Ceylon, discontent with what she believes to be overly lenient policies by her predecessor as St. Gloriana's commander, becomes very harsh in her leadership of the team, to the point of being abusive. The team advances to the semifinals, but is defeated as a result of one of Ceylon's mistakes, and partly the result of a mistake made by one of her panicking subordinates; Ceylon tries to scapegoat the latter for what happened. In the end, Ceylon leaves the school as a pariah, and leaves high school feeling empty.
Film - Animated
In Pixar's Cars, Chick Hicks wins the final race, but because of his actions during it, he finds himself hated and rejected by everyone.
Film - Live-Action
Michael Corleone might be the ultimate example of this by the end of The Godfather Part II. Certainly he's destroyed every major underworld power in his way and taken on the US government and won, but he's also destroyed his marriage, alienated his children and friends, killed his brother, and is left utterly alone. And then the third film features his daughter getting killed right in front of him.
Daniel Plainview's empty isolation and drunken insanity at the close of There Will Be Blood. And his now immortal final line: "I'm finished!" implies that the way his life turned out is exactly what he wanted.
The movie version of The Talented Mr Ripley has Ripley having to kill everyone he likes in order to get away with it. The book ends by indicating that he'll never be able to look at another policeman without that flash of alarm that says "This is it — he's the one — he knows." Not a way anyone would like to live life.
Star Wars: Anakin Skywalker is a prime example of this by the end of the prequel trilogy in Revenge of the Sith. Sure, he's won the war, and his turn to The Dark Side has allowed his Evil Chancellor partner to take over the galaxy, but he's lost the pregnant wife he did it all for, had his limbs chopped off, is forced to spend the rest of his life in an uncomfortable life support suit to avoid dying from his burns.
By the end of 300, Xerxes has lost most of his best troops and although he's defeated Leonidas at Thermopylae, the performance of the Spartans and the losses inflicted among his men has only given new determination and inspiration to the other Greeks. Historically speaking this was only a minor setback for the Persians, but other Greeks counterattacked and forced the Persians to leave the country; therefore Xerxes won the battle but lost the war because the chokepoint of Thermopylae bought the other Greeks enough time to mass for their counterattack.
By the end of Pat Garrett and Billy The Kid, it's clear that Garrett realizes that he will lead a conflicted, unhappy life and will be chiefly remembered for killing his friend. Billy, meanwhile, will have most of his bits of sociopathy forgotten by an adoring public. (To an extent, this extends to other portrayals of the two, including Young Guns 2).
In Lord of War, Villain Protagonist and Arms Dealer Yuri Orlov manages to evade the law and escape a long stay in prison to continue his gunrunning. However, this comes at the cost of his brother and uncle being killed, his parents disowning him, and his one true love divorcing him and taking his only son with her. He was also released only due to being useful to the U.S. Government and he's fully aware they can have him disposed of if his usefulness ceasesnote such as if the political liability of retaining him finally overrides the de facto benefit of his services. This is hammered home when the Interpol agent chasing Yuri says that normally he'd tell Yuri to go to Hell, but he thinks that Yuri's already there.
Real Steel has Zeus declared the winner of the match between him and Atom despite the latter knocking the former out, keeping his status as the unbeatable champion. However, Zeus is booed by the crowd who embraces Atom as the "people's champion."
In The Avengers, Tony tries to explain to Loki that this is the best he can hope for.
Tony Stark: You're missing the point! There's no throne. There is no version of this where you come out on top. Maybe you open the portal, and maybe your army is too much for us, but it doesn't matter. Because whatever happens, it's all on you. Everybody will be gunning for you. Because if we can't save the Earth, we sure as Hell can avenge it.
In the Chuck Palahniuk novel Haunted 2005, one character, a small time journalist, tells a story about bringing his sick dog to a strange vet and realizing the vet is a former child star. He does a friendly interview with the vet, which shows the vet has made a good, happy and normal life for himself, but the tabloids the journalist works for aren't interested in it. They don't care about former stars that are normal and happy. So he talks to the vet again, drugs him, makes him OD, and creates a wild story about the former star having sex and drug addictions, etc. The story sells and earns him a ton of cash... but next week when his dog is sick and he doesn't know a good vet to bring it to, the dog dies.
Judas Iscariot may be an example. Sure, he got a tidy sum for betraying Jesus, but, according to Matthew, he was so overcome with guilt afterwards that he hanged himself.
Exactly how things worked out for Judas varies a bit depending on who's telling it. The Gnostic Gospel of Judas (rejected when New Testament's contents were formalized) even claimed that Judas "betrayed" Jesus under Jesus's orders.
Jesus said, "Truly, I say to you, one of you will betray me, one who is eating with me... For the Son of Man goes as it is written of him, but woe to that man by whom the Son of Man is betrayed! It would have been better for that man if he had not been born." (Mark 14:17 & 21, ESV)
And of course, that "tidy sum" of earthly treasure is mere pittance compared to the honor his fellow apostles would have of "sitting on twelve thrones, judging the twelve tribes of Israel", not to mention sharing in the same inheritance that the Lord and His believers would receive from His Father. To compare it to another part of the Bible, Judas' thirty pieces of silver is the equivalent of Esau's bowl of pottage which he traded his birthright inheritance for with his brother Jacob, which brings us the Aesop that sacrificing one's future (heavenly) inheritance in exchange for the satisfaction of immediate short-term (worldly) gain isn't a good thing.
In Test of the Twins, Raistlin Majere's goal of becoming a god is revealed to be a severe case of Pyrrhic Villainy. He succeeds, but in the process he destroys the world and eradicates every shred of good in his own soul, leaving him with no ability to renew or heal that which he has laid waste. Fortunately for all concerned, his brother Caramon is able to go back in time and reveal this outcome to the earlier Raistlin, who then sacrifices himself to save Caramon and Crysania.
He thinks of it differently, as revealed during his nephew's test to become a full-fledged mage.
Raistlin: I sacrificed myself to save myself.
In the William Gibson short story "Dogfight," the main character wins the aerial combat video game, but in the process alienates everyone he might possibly celebrate his victory with.
The Silmarillion: after 500 years of struggle, Maedhros and Maglorfinally get the two remaining Silmarils. In the process, they lost their father, all their brothers, their kingdoms, their followers and, thanks to them committing genocide against other elves on three separate occasions, they've made enemies of the entire world, and they reject the Last-Second Chance offer for them to return to Valinor for trial (where they may eventually be reunited with their dead family). And when they try holding the Silmarils in their hands? The gems burn them due to all the evil they've done, so they can't even hold them without feeling unbearable agony. Maedhros ends up throwing himself off a cliff with his Silmaril, while Maglor throws his away and spends the rest of his days Walking the Earth lamenting their folly, too ashamed to ever face another living being again.
Sure, by the end of PLAGUE (4th GONE book), Caine Soren finally got that important position of evil dictator he was pushing for since book 1, but at what cost? Oh yes, A) He doesn't really have supreme control at all. B) Everyone hates and disrespects him. and C) the love of his life just left him for his twin brother/arch enemy. And she's pregnant with his demon child, who certainly stirs shit up for him later. Some victory that turned out to be.
Tywin Lannister destroys the Starks as a noble house. In the process, his eldest son is crippled by Tywin's own mercenaries and later denounces him, Gregor Clegane renews tensions with Dorne, his last-minute Tyrell allies poison his grandson and take a large chunk of his political power and he is then ignominiously killed on the toilet by his abused younger son.
The Freys gain possession of Riverun and a number of other perks for perpetrating the Red Wedding. They're currently the most despised house in Westeros and are being killed one-by-one by the Brotherhood Without Banners and Wyman Manderley. There's also signs that tensions within House Frey's itself is beginning to reach boiling point and should Lord Walder Frey finally pass away, the Frey's are expected to implode.
Roose Bolton becomes one of the most powerful men in Westeros for betraying and murdering Robb Stark. He also inherits Robb's war with the Greyjoys, a war with Stannis, the imminent invasion of the Others and only a handful of Roose's new vassals aren't actively plotting against him. Additionally, his years-earlier rape of a miller's wife turns out to bite him in the ass in the major way when Ramsay, the product of said rape murders his legitimate son Domeric, thereby becoming his heir by default, and potentially undermines Roose's gains with his out of control sadistic behavior, including his treatment of the fake Arya Stark they have him marry to cement the North, whose cries from her tower embolden the remaining residents of Winterfell towards a possible coup.
Live Action TV
The Wire: after killing and backstabbing his way to becoming Baltimore's chief drug kingpin, Marlo enjoys it for only a month before losing his entire organization and being forced to go straight by the police. His name and reputation, the things he treasured most in the world, are quickly forgotten while his defeated enemy Omar lives on as a street legend.
The Shield's Vic Mackey ends up with a cushy job as a Federal Agent, after burning every bridge imaginable with his family (disowned him and in witness protection), his friends (one killed his entire family/self and left a note blaming Vic for turning him into such a monster while the other, whose loyalty to Vic was never in question, was made into the scapegoat for Vic's crimes), and pretty much had ALL of his sins exposed to the world, as part of an immunity deal he landed as part of his job. Worse, his cushy job is a desk job, which plays against Vic's strengths as a law enforcement agent and his boss, horrified at the fact that Vic conned her, has vowed to make Vic's life a living hell in a desperate hope to make him void his immunity deal, costing him his job and freedom. And even if he survives, after three years, the Feds can fire Vic, and with his sins all public knowledge, this means that Vic will never gain employment in law enforcement again, denying him the justification he used to hide from his crimes. Karma is a bitch, Vic.
Lucas North from Spooks. He succeeds in selling the Albany file to the Chinese, but in the process destroys the life he built and causes the death of the woman he loves. And to top it off, the weapon Albany is a blueprint for turns out not to work.
Morgana from Merlin lives for vengeance, but when she finally manages to have King Uther killed, it's clear that she doesn't feel the victory the way she thought she would.
In the Star Trek episode "Let That Be Your Last Battlefield," the ship is occupied by two aliens from a species where half are black on their right side and white on their left, and the other is the opposite, and the former have set themselves up as the societal superiors of the latter, in an obvious metaphor for the racism prevalent at the time. The black-on-the-right one is chasing the white-on-the-right one as a criminal, and ultimately succeeds in forcing the crew to return to his home planet, where his prisoner can be judged. However, they find that while the chase was going on, the war between the two sides escalated until every single person on the planet was killed. The two aliens promptly accuse each other of their people being responsible, and teleport down to the planet to continue their war, as Kirk somberly notes that their hatred for each other is all they have left.
Walter White of Breaking Bad manages to slip the law, his competitors and former allies in the drug trade. Each time he does it ruins the lives of those around him and costs him a little more of his soul. By the end of the series he finally secures millions of dollars for his children and dies on his own terms. In the process, among other tragedies, his brother-in-law is murdered, his partner is almost psychologically destroyed, his wife and son despise him, two children are murdered, he inadvertantly helps to cause a plane-crash and his criminal life becomes national news.
Kratos in the first God of War (Back Story included) gains a great deal of power at the cost of many lives, kills the original God of War, Ares, and becomes the new God of War in the process. Unfortunately for our Sociopathic Hero protagonist, his burning ambition costs him the lives of his family (by his own hand), possibly the only thing he genuinely cared about emotionally, and causes him to go nearly insane with guilt and endless nightmares. After learning that all of his efforts towards his goal of ending said nightmares were ultimately futile, he, despite everything that he had gained, descended further into madness (leading to the events of God of War 2), where he ends up killing Athena, the one Goddess who was sympathetic to him..
The third game ends Kratos' story in this manner. Kratos finally has his revenge on Zeus, and has brought down nearly all of Olympus AND the Titans. However, each god he killed caused a major calamity to strike the world. By the end, the oceans have risen (Poseidon), the sun has been blotted out (Helios), a plague has broken out (Hermes), all vegetation has died (Hera), and what little remains has been covered in Gaia's remains. Even worse, Pandora's Heroic Sacrifice (something he was trying to prevent) was utterly pointless, as the power to defeat Zeus was in him the entire time. When Athena's ghost pulls her Face-Heel Turn, he finally has had enough and impales himself, which releases Hope and helps the world a little... but he's still dead, and can never rejoin his family. Damn.
Or is he? Waiting through the credits reveals Kratos may be alive.
At the end of Final Fantasy Tactics, Delita successfully manipulates his way to absolute power over Ivalice, destroying all of the competing factions and ascending to the throne by seducing and marrying Princess Ovelia. Unfortunately, his methods so thoroughly alienate his new bride that she decides she must have been part of his machinations too, and stabs him, possibly fatally. (If the cutscene writers didn't pay attention to Delita'sunarmouredHPat least...) This forces Delita to kill her in retaliation, and he is left wondering if it was all worth it as he falls to his knees clutching his wound. (The painfulness of this scene is increased further if you believe that Delita genuinely loved Ovelia.)
One of two inevitable outcomes of Nuclear War (the DOS game by New World Computing, not the actual political option). Either the last remaining ruler on Earth presides over a blasted wasteland, or the entire world is destroyed.
In the first Kingdom Hearts game, Ansem (who you find out, in Kingdom Hearts II, is really Xehanort's Heartless), successfully opens the door which he believes would lead to ultimate dark power; however, Sora tells him that "Kingdom Hearts is Light", and the villain ends up getting disintegrated when the door opens.
In Dragon Age: Origins, Well-Intentioned Extremist Teyrn Loghain's plan to take the throne of Ferelden works like a charm ... up until the point where it sparks a civil war and causes riots throughout the country. Ironically, in an effort to protect Ferelden from Orlesian occupation, he's forced to act just as badly as the former conquerors he once struggled against. This sends him into a deep depression and eventually sparks a Villainous Breakdown.
Happens to Bhelen Aeducan should he gain the throne of Orzammar, if the player is the Dwarf Noble. Bhelen murdered his eldest brother Trian and framed the Dwarf Noble for the crime, stripping their name and sentencing them to exile in the Deep Roads. Because of the loss of his two children (although it's implied poison may have been a factor), their father died, leading to a Civil War when the Dwarven Assembly were divided over who should then take the throne. The Dwarf Noble returns to Orzammar, having now become a legendary Grey Warden, and proceeds to end the stalemate by seeking out a Paragon in the Deep Roads, thus leaving Bhelen to suffer being handed the throne by the very sibling, whom he had sent to die. To add further insult to injury, after ending the Blight, the Dwarf Noble is named a Paragon by the Assembly, which restores their name to the Orzammar histories.
In Fallout: New Vegas, one of the ways to talk down LegateLanius in the Final Battle is to convince him that even if he were to beat the NCR and conquer Hoover Dam, the Legion would inevitably fall via attrition (due to Rape, Pillage, and Burn being a poor long-term way to sustain an army) or overextending themselves (much like the NCR themselves have done).
At the end of Batman: Arkham City, when it looks like Batman might not saveThe Joker from his TITAN poisoning the clown backstabs him to try getting the cure, causing it to drop and smash on the ground. Joker dies about a minute later. Extra irony-points because Batman really would have saved the Joker, and in his dying breath, he finds that fact hilarious.
Dr. Eggman's plan actually succeeds in Sonic Riders... kinda. He does manage to steal the treasure of Babylon, which turns out to be a rug. He faints when he realizes how much effort he put into it. If he'd kept it, he could've discovered that it was actually ancient Babylonian technology that actually flies.
This gets referenced in Sonic Generations, when Classic Robotnik asks Eggman if he's ever won, Eggman responds "Depends on your idea of winning."
Vaarsuvius's Deal with the Devil, literally harnessing the powers of evil, ultimately doesn't accomplish what they planned. In a twist, V's subsequent actions cause a LOT of change, some of it even good, but they're left morose at how badly things went awry. Thankfully, this has started V down some real character development.
The final Act of Doctor Horrible's Sing-Along Blog, Joss Whedon's 2008 Web Original supervillain musical. Dr. Horrible, attempting to kill Captain Hammer to both gain entry to the Evil League of Evil and win Penny's heart, indirectly causes Penny's death and Captain Hammer's humiliation. The final scenes show him living the high life of an A-List villain...but the final shot shows Billy, heart-broken and traumatized. And the final song describes that he has achieved everything he ever wanted, but the lyrics are dripping with double meanings: "The world I wanted at my feet": the world is my oyster, or Penny - the "world I wanted" - lying dead at his feet.
Bennett The Sage and JesuOtaku have done several crossover videos, with the idea in mind being Bennett attempting to Break or Corrupt the Cutie with terrible and sexually shocking or exploitative anime. The third time around, during Jesu's review of Master of Martial Hearts, she agrees that Sage has won and shown her something so gratuitously cruel and horrific that she just can't laugh it off or remain unaffected by it. However, after a relatively short spell of being horrified, she remembers that it was just fiction and all the good things about life, and goes outside to enjoy herself and play with her roommate's dog. Sage is left in a depressive funk with his "victory", pondering where mankind has gone wrong, whether a species capable of such things is worthy of redemption, etc.
Villain on villain case: in Batman: The Animated Series, the Corrupt Corporate Executive whose unfair treatment first turned Edward Nygma into The Riddler succeeds in continuing to make money off Nygma's intellectual creations, but lives his life in constant paranoid fear of Nygma coming to get him again.
Batman Beyond does a similar thing with Inque's daughter, who screwed her over and tried to kill her. She now lives in fear of the vengeance of the assassin who can be anywhere, as anyone or anything, seeing her in every shadow.
In a milder example, Jervis Tetch (the Mad Hatter) in Batman: The Animated Series uses his mind control technology to land Alice, a co-worker he was too shy to talk to, but Batman calls him out on this, asking if a mind-controlled, compliant Alice with no personality was what he really wanted. Tetch has a breakdown and lets her go.
Speaking of Batman, Batman: The Brave and the Bold ends with Bat-Mite screwing over the show to get it cancelled so that a darker, more serious Batman series will be made in its place. The new series focuses primarily on Batgirl, and as Ambush Bug points out, a serious Batman series has no room for Silver Age silliness... like Bat-Mite himself. Bat-Mite realizes his mistake seconds before he is erased from existence.
Justice League had an episode where Superman is transported thousands of years into the future, only to find the immortal Vandal Savage as the sole survivor of the human race, thanks to his use of an ultimate weapon. He's had plenty of time to reflect, alone, about how utterly unimportant ruling the world is. He even tried to build himself a spaceship, but stopped when he realized he deserved to be punished. Superman leaves to stop "his" version of Savage from building the aforementioned weapon, but with a new-found respect for the villain. Given that this was Savage's last appearance on JL, it can be assumed that Superman shared some of what he'd seen with the modern day Savage, and convinced him to turn away from his life of villainy.
Frequent theme in The Venture Bros., but in one specific example, the Monarch has kidnapped Hank and Dean and is holding them for a ten million dollar ransom, threatening Doc Venture that if he doesn't pay, some giant mechanical caterpillars will "destroy the only proof he's ever had sex."
Doctor Girlfriend: How much did the caterpillars cost?
Monarch: A couple of mils.
This may be an inversion: to the audience and everyone in the Venture universe, the Monarch's actions seem Pyrrhic, but the Monarch himself considers whatever cost he has to pay in order to destroy/inconvenience Dr. Venture absolutely worth it. In his twisted mind, those caterpillars were money well spent.
It's also unclear how taxing a price that is to the Monarch. It's never stated just how much money he has, but he's been consistently referred to as being wealthy. A couple of mils might be well within his budget.
It was mentioned in that show that the reason he was asking for a ransom, which was against the usual guild rules, was that they were low on money.
Actually, it seems more Monarch was ransoming the boys since he was well aware of Venture's money woes, and since his psychological torment seems to fall flat most of the time, he'd try torturing his wallet, though according to later episodes the Cocoon funds are running low, at least not enough to afford a small army's worth of body armor.
In Wakfu, Nox has spent 200 years of research, plotting, and genocide in order to gather the energy needed to travel back in time and stop his family from being destroyed partially due to his own negligence. In the end, he manages to defeat the heroes, drain the Tree of Life (killing the Sadidas in the process), and uses the all the energy gained over this time period to travel back in time... a whole twenty minutes.
Total Drama World Tour: Courtney finds out Gwen and her boyfriend Duncan kissed and vows revenge. She gets support from most of her team and eventually Gwen is voted off. However, Gwen and Duncan remain a couple, while Courtney loses support from her team, fails in getting Duncan voted off, and gets voted off herself instead. And most of all, she blindly falls for Alejandro, who is just using her, and he loses anyway. So in the end, Courtney ends up with nothing and no one.
Jimmy Two-Shoes. Lucius manages to push the weavils off their land, but the mountain he was going to carve his face into ends up carved into a weevil head instead.
In the episode "The Super Speedy Cider Squeezy 6000", the Flim Flam Brothers win the contest with Applejack by producing far more barrels of cider than she and the rest of the Mane 6. In the process, they not only manage to alienate the town with their Jerkass behavior, but also had to shut off the quality assurance of their machine to win. The resulting cider is so unappetizing that nopony is willing to buy or take it for free. Faced with an angry mob, they have no choice but to pack up and leave.
In "Rarity Takes Manehattan", Suri takes credit for the creation of Rarity's special fabric to up her reputation at a fashion competition. She does end up keeping Rarity from reaping the benefits of the competition and it's never discovered that she didn't make the fabric herself. But on the flip side, Rarity manages to still officially win the competition, Suri's Hypercompetent Sidekick (who did most of the actual work) quits and does a Heel-Face Turn, and while she has the reputation for making beautiful fabric, she doesn't have the actual ability, meaning that her reputation will be short-lived.
In the TRON: Uprising episode "Rendezvous", Pavel repeatedly frames various programs, and ends up promoted to the overseer of a district. The district in question? Purgos! And not only does Tessler expect Pavel to clean it up, Paige knows exactly what Pavel has been up to and tells him that she'll get him back for what he did. And on top of all this, Pavel had to hand over the upgrade Disc he'd been hiding!
In The Fairly OddParents special "Timmy's Secret Wish", Foop succeeds in making Timmy look like the worst godkid ever and having all his wishes undone, including Poof. However, he learns too late that as Poof's anti fairy, he gets erased from existence too. This brings Ascended Fridge Horror into play when many wondered what would happen to Foop if he succeeded in erasing Poof.