Genocide Backfire

"Freeza: You...you...what are you? Goku: You haven't figured it out yet? I'm a proud Saiyan who calls Earth home, and I'm here to defeat you. I am the warrior you've heard of in legend, pure of heart and awakened by fury. That's what I am. I AM THE SUPER SAIYAN, SON GOKU!"

- Dragon Ball Kai

A type of Villain Ball, and subtrope of Laser-Guided Karma.

Here's the deal: you're the Evil Overlord. You're in charge and like it. But something's been nagging you. You're worried that one day you might lose your position by force. Furthermore, it looks like there's good reason, 'cause there's a prophecy involving someone from "Insert Name Here-istan" who's going to take you out.

Screw that! You're the villain! You're keeping your position and no brat is going to take that from you. If it means killing every last Insert-Name-Here-istanian and putting their heads on a pike, so be it!

16-30 years later, you find yourself at the mercy of the last son of "Insert Name Here-istan", and he's kinda pissed that you skewered his family. Sometimes, you are in this situation because you committed this genocide since you set in motion a series of events where that infant is taken to a place where he is not only kept safe, but the natives there help him become a powerful warrior ready to take you on. Furthermore, if you are stupid enough to continue your villainy with grand schemes of bloody conquest, that hero will likely be spearheading an overwhelming army of friends determined to bring you to justice.

Goddammit!

This trope is when the bad guys (or the supposed good guys) commit a massive atrocity to achieve some goal, only to not completely succeed, and the resulting incompleteness comes back to bite them in the ass.

It often involves a prophecy, and this is the villains' attempt to "Screw Destiny". For all the good it does them.

This typically means murdering hundreds of people to kill a single child, who will inevitably escape -- see Nice Job Breaking It, Herod. Sometimes, the evil overlord might live out his life successfully, but his descendants pay the price.

There are two main variants:
 * 1) The first is that a prophecy says that someone from the time/place will overthrow them.
 * 2) The second is that the victimized people pose a threat and this is a means to deal with said threat.

A third, less common type involves the overlord's minions, being not that evil, decide that this is a Moral Event Horizon they will not cross and their boss is too evil to work for.

Expect the survivor to benefit from What Measure Is a Non Unique, using his heritage and tragedy to fuel the coming Roaring Rampage of Revenge (or the even more tragic Cycle of Revenge). Sister Trope to Nice Job Breaking It, Herod, with which it can overlap when the motivation behind the Genocide is finding and killing particular individuals.

It is sometimes called the "Dandelion of Doom" or "Dandelion effect," per the expression: "If you kick a dandelion, you spread its seeds." Just as this is an ineffective way to remove weeds from a lawn, it is an ineffective measure to remove potential threats to one's rule.

Please, let's not involve Real Life in this.

Anime and Manga
"Vegeta: So, you tried to eliminate the Saiyans, yet you left the strongest one alive! Smooth move!"
 * Frieza exterminated the Saiyan race in an attempt to prevent any from potentially becoming the legendary Super Saiyan. He missed four. Two of them, Radditz and Nappa, worked for Frieza alongside Vegeta, the prince of the Saiyans, but Goku, the fourth, would eventually take Frieza down by becoming the very thing Frieza feared. What's more, after getting turned into a cyborg and coming to Earth to take revenge, both he and his father King Cold are taken down for good by Future Trunks, who turns out to be the son of Vegeta, the other major Saiyan to survive.
 * DBZ, the manga (Goku was last) and anime (Broly was last) canons, qualifies through Goku. Goku was only there due to a plot by Vegeta to overthrow Frieza due to this trope.
 * Vegeta even Lampshades this shortly before Frieza transforms into his second form.


 * In Hunter X Hunter, this seems to be creeping up on the Phantom Troupe, who murdered the entire Kurta clan, maimed their corpses by removing their pretty eyes to sell them, and treat it as no big deal, which further angers the last surviving Kurta, Kurapica. Kurapica has already killed two of their members, and is quite intent on finishing what he started.
 * On top of that, if it weren't for some timely intervention from their leader, Kurapica would've killed 6--half of the entire group by the time he killed the second. That's how big of an enemy they've made.
 * Bafflingly Averted Trope twice in Naruto. Evil Overlords Orochimaru and Pain cement their statuses as village leaders by rolling in and completely demolishing the leaders, family, and government of their respective countries--implied in Orochimaru's case, outright stated in Pain's. This works out very well for them, mostly because they actually succeeded in subverting Infant Immortality. Both do end up meeting their ends, but for reasons unrelated to their murderous ascension to power.
 * It helps that Salamander Hanzo was a complete monster himself, so the Rain Country sees Pain as a hero, and they know nothing of the Akatsuki or the abduction of Jinchuriki and fatal extraction of their Biju that Pain is partaking in, or of what he plans to use them for. As for Orochimaru, as stated above, there isn't much information about the Rice Pattie land's politics, and he probably started the Sound Village.
 * Also deliberately invoked by It still falls through, though;
 * The Ishvalan Genocide from Fullmetal Alchemist is an interesting case. The purpose of the extermination was not to prevent a prophecy from being fulfilled or to dispose of a threatening ethnic group per se, but to simply kill as many people as possible - their aim was to kill every Ishvalan, but as you would expect, there were some survivors. Now, one of those survivors was Scar, whose brother was killed in the extermination and who was determined to revenge his death to the State Alchemists... that is, in the beginning.
 * And in the first anime, the purpose was -- something Scar . Meanwhile,
 * In Yu-Gi-Oh! Millenium World Arc, the Millenium Items were a result of an alchemical ritual that involved sacrificing an entire village through genocide. Unfortunately for the priests of the pharaoh and the civilians 3000 years later, they forgot to kill the young.
 * In Bleach, there was a disagreement among the Soul Reapers and the Quincies about how to handle wayward and malevolent spirits called Hollows, which ended in the Soul Reapers killing off every Quincy they could find. Fast forward to the present, and the revenge-filled Quincies who survived the massacre.

Comic Books

 * In the comic version of Wanted, the Big Bad Mister Rictus deliberately invokes this trope, though on a much smaller scale. After murdering an entire family, he leaves a single child alive, banking on the chance that he will grow up to try and take revenge on him. Yes, Mister Rictus really is that bored and crazy.
 * The Sonic the Hedgehog series had this for its Endgame storyline: Dr. Robotnik uses the Ultimate Annihilator to erase Knothole from existance in front of Sonic. A combination of Snively's backstabbing, a mini nuke and Sonic's own two fists ensures that Knothole is restored and Robotnik's done away with permanently.
 * An interesting variant in one Sandman story, it's implied that Despair organises the destruction of Krypton, but decides to leave a single Kryptonian alive, assuming that he will spend his entire life mourning his lost world in despair. That Kryptonian grew up to be Earth's greatest hero, and a symbol of hope to billions of people, so Nice Job Fixing It, Villain.

Film

 * A variant with a twist in Lexx; the Divine Shadow orders the destruction of the Brunnen-G homeworld in order to thwart a prediction that the last of their race would destroy him. He actually completely succeeds in wiping out the entire planetary population, but decides, with his victory accomplished, to mock the prophecy by turning several of the corpses into an undead immortal killing machines under his control. Centuries later, the last of said corpses ends up regaining his memories, killing him, and bringing down the entire Divine Order.
 * In The Chronicles of Riddick, the Lord Marshall of the Necromongers tries to wipe out the Furyan race, due to a prophecy that a Furyan would kill him. He misses (at least) two of them; the titular Riddick is one of them.
 * In The Dark Crystal, there's a prophecy that a Gelfling will undo the damage to the Dark Crystal, ending the reign of the Skeksis, so of course they go off on a Gelfling killing spree. One of the Skeksis himself, (pretending to be friendly) says "Prophecy! Prophecy caused all this trouble!"
 * In Tron: Legacy,  Not quite a genocide backfire since
 * Star Wars, of course. They didn't kill Anakin and Padmé's children. Nor did they kill Obi-Wan. They didn't even kill Leia when they killed all the other Alderaanians. This did not work out well for Palpatine.
 * It's not genocide, but the Jedi invoke a version of this trope themselves. For thousands of years, Jedi were trained from infancy in order to avoid the complications and risks (for force users) of emotional relationships and personal attachments. Then along comes the potential prophesied child and they decide that, this one time, because of the circumstances and the Dying Wish of Qui-Gon Jinn, they'll take in this little emotionally battered former-slave child (abruptly taking him from his mother who he is never allowed to see again). That one came back to bite them in the ass. HARD.
 * This seems to be a cycle in the expanded universe: Jedi vs Sith war ensues, the Jedi win, the Sith are exterminated. The few Sith survivors hide and refound the Order in secret, then they attack the Jedi again, win and the Jedi are exterminated. The few surviving Jedi hide and refound the order in secret and counter attack the Sith. Lather, rinse, repeat. Apparently nobody noticed yet that, whenever Jedi or Sith are almost wiped out, they return much stronger.
 * Occurs in Kung Fu Panda 2, overlapping with Nice Job Breaking It, Herod; Lord Shen is told a prophecy that he will be defeated by a 'warrior of black and white', and decides that the correct way to respond to this is to commit panda genocide. Played with later on when Shen first meets Po, and is a little surprised to find that said panda had no idea what he had done.
 * Slightly subverted at the end, which shows.
 * In The Scorpion King, the titular protagonist was one of the few survivors of Memnon's genocide of the Akkadian people. Shortly after the beginning of the film, he ends up being the sole remaining member of his people. Turns out, he is the one who was prophesized to take Memnon down.
 * It's never explicitly stated that the Akkadians were wiped out by Memnon's forces. Given the fact that they were mercenaries, it wouldn't make much sense for him to get rid of such warriors, when all he had to do was pay them.

Literature

 * In The Graveyard Book this is the reason why.
 * Arguably happens in Dune, where
 * In R.A. Salvatore's Forgotten Realms novel Homeland, one Dark Elf house in Menzoberranzan is punished for failing to kill off all of a rival house's noble family by the Deadly Decadent Court, which sentences the attacking house to be exterminated properly. This is built into their "law"; total extermination is fine, just don't leave any witnesses. Of course, only surviving nobles count as witnesses, not ordinary underlings. Wouldn't want to actually discourage competition, now. And it would be a waste of people to kill everyone.
 * In the novel Talon of the Silver Hawk, the eponymous character is almost the Last of His Kind, and ends up working (under the name Talwin Hawkins) for the guy who ordered it in a long-term plot to bring him down.
 * Played with in Jack Vance's The Demon Princes. The hero wouldn't have had any reason to devote his life to tracking down and killing the titular villains if they had chosen a different space colony to raid on that day.
 * Also different in that it was the other survivor, his grandfather, who groomed him to be an instrument of justice. The hero may have just gone off to life peacefully somewhere else if given the chance early on.
 * In the first book of Laurie J. Marks' Elemental Logic series, a whole tribe is killed off because of a prophecy that indicates Bad Things for the invading army if a single member of the tribe survives. Of course, one (and only one) tribe member escapes...
 * In C.S. Friedman's Coldfire Trilogy, the immortal and extremely narcissistic Magnificent Bastard character of the series left one of his children alive when he slaughtered his family to make a pact with a demon. Over the next thousand years he would occasionally go back and murder all of his descendants, again except one. He was vain enough that he had to leave alive the one descendant who looked the most like him. Of course,
 * Not quite. His descendants were free to live without being troubled, provided they never ever laid claim to his title as the Neocount of Merentha. If any of the male descendants did so, then The Hunter would again lay waste to his entire family, save one.
 * In Jacqueline Carey's The Sundering, the Anti-Villain Satoris wipes out a desert tribe that sent a child to destroy him. Unusual in that the child had already been dispatched by that point; however, he had nothing in particular against Satoris until his village was destroyed, and it's strongly implied that he could have been talked out of his quest if that atrocity hadn't been committed.
 * It's implied that Garoth Ursuul of The Night Angel Trilogy commits genocide often enough that he actually has a list of rules, among them is "You will always miss one." This is never shown to actually come back to haunt any Ursuuls in the book, however.
 * Happens lots of times in David Weber's Empire From the Ashes, as the omnicidal Achuultani, themselves a last remnant from a campaign of genocide by a hostile power in their own galaxy, have nearly wiped out humanity several times. We now have planetoid dreadnoughts whose star drives can cause supernovae when used too close to a star, and each has combat capability equivalent to hundreds of thousands of Achuultani ships. Oh yes, and we know where they live.
 * Implied at the end of Out of the Dark, again by David Weber. The Shongairi announced themselves to Earth with a series of Colony Drops on Earth capitals, and when controlling Earth proved to be impossible tried to exterminate mankind with a biological weapon. They failed, and at the end Humans knows how to replicate Shongairi technology and where they live.
 * A small-scale version of this is the core plot of Mercedes Lackey's first Vows & Honor short story Sword-Sworn. A large force of bandits, with the aid of a wizard to strike down the sentries, ambushed the Shin'a'in clan Tale'sedrin on the way back from a horse fair and killed every one of them... save the skinny teenager they did not bother making sure of after strangling and gang-raping her.
 * Last Legionary: The Big Bad deciding the Legions of Moros were the major obstacle to him conquering the galaxy and that eliminating was the best course of action? Doesn't work out so well. The Legions weren't even aware of the Warlord's existence prior to the attack that left Keill the only survivor of his race.

Live Action TV

 * On Doctor Who, the Doctor has attempted genocide on the Daleks at least four times. It never takes.
 * He did deliberately avoid committing genocide in Genesis of the Daleks, giving as his reason that while the Daleks are indeed evil, omnicidal Space Nazis, a lot of good has come out of people banding together to fight them. That decision sure came back to bite him in the ass.
 * After the Doctor supposedly wiped out the Daleks and Time Lords when the Time Lords were prepared to destroy time itself, one more Time Lord managed to escape the War some time before.
 * Played with in Chikyuu Sentai Fiveman where the Big Bad was defeated by the flower of the first planet he wiped out (he forgot the memo to destroy it completely).
 * Near the series finale of Star Trek: Deep Space Nine, the Cardassians have at that point lost all standing with the Dominion and are not much more than unwilling vassals. This leads elements of the the civilian population to subvert the Dominion war effort through acts of sabotage. As a result of one particular incident which nearly cost them a battle, the Female Changeling orders a major Cardassian city to be wiped out by orbital bombardment as an example, and announces that the Dominion will destroy one city for every act of sabotage committed. After hearing this, however, the entire Cardassian fleet does an abrupt Heel Face Turn in favor of The Federation instead, as well as getting many Cardassian soldiers on-planet to defect. This in turn prompts the Dominion to to start slaughtering the Cardassians en masse, but since her subordinate proceeds to send out most of their troops stationed at the base to do so, this leaves their installation critically under-guarded when Damar and his crew attack Dominion Headquarters.
 * Irony time: the Cardassians used the same tactics during their earlier Occupation of Bajor, with the same results (except they were smart enough not have Bajorans fighting alongside them on the front lines of an interstellar war at the same time).
 * Star Trek: Voyager had a variant: The Krenim were going around exterminating entire races from the timestream to make it as though their empire never fell. Unfortunately, this was a hit or miss endeavour. Sometimes, it resulted in their empire at near full strength, others it set them back centuries. But the first backfire that happened was that one of the races that helped destroy their empire in the first place also introduced some disease treatment that without which caused the death of the project lead's wife, and none of the altered timestreams had a cure. Since then, the project lead was desperately searching for a way to fix things for his own ambitions.
 * In Stargate: Continuum, Baal is Genre Savvy enough to know that trying to exterminate the Tau'ri will only cause eternal resentment among the survivors who will try and take revenge. Instead, he tries to woo humanity to his side peacefully with the intention of turning them into the next generation of Jaffa. Unfortunately for him, his wife didn't quite see it that way, and decided to do a bombardment of the planet after murdering him.
 * In a first season episode where Daniel lands in an alternate grimmer dimension where the Goa'uld have invaded Earth, an cold-hearted O'Neill sends a nuke to the Jaffa homeworld upon learning the location from Daniel who wanted. This bites him in the ass when he pleas Teal'c to think of his son, who has been killed by the attack.
 * Tried by Darken Rahl in Legend of the Seeker. He got wind of a prophecy that the True Seeker would be born in a certain town, so he had his troops, led by his most trusted lieutenant, to kill all the first born sons in the town. Sure enough, Richard was spirited away, and when Rahl finds out 20 years later, he executes the lieutenant.
 * A very longterm example occurs in the Babylon 5 universe. The Hyach once shared their planet with another sentient species, the Hyach-do. The two races coexisted peacefully for thousands of years, and even intermarried, until the Hyach exterminated the Hyach-do in a frenzy of religious fervor. Centuries later, it was discovered that the declining birth rate of the Hyach is because interbreeding with the Hyach-do was necessary to sustain the Hyach genome. Thus, in wiping out the Hyach-do, the Hyach have doomed themselves to extinction as well.
 * In Lexx His Divine Shadow was very thorough in wiping out the Brunnen-G, but he made the mistake of reanimating the last one.

Mythology and Folklore

 * King Arthur learned that he would be destroyed by a child born in a certain month, he had all the babies from that month gathered together, put on a ship and sent to die. The ship crashes and kills every one of them... except for one: Mordred. This is one of the newer versions of the much-revised legend, however. Earlier versions of the story have Mordred as his nephew, there is no such genocide, and Lancelot is nonexistent.
 * In one more recent version, a Genre Savvy King Arthur knows how a Genocide Backfire works and instead conscripts all the boys of that age group and makes them squires. All of them but one love him. The one? Mordred.
 * The Kalevala has this: Untamo kills his brother Kalervo and his clan over petty neighborhood squabbles, leaving only a pregnant woman alive. The woman in time gives birth to Kullervo, who later kills Untamo - and wipes out his clan, for good measure.

Tabletop Games

 * In Rokugan, the setting of Legend of the Five Rings, the Scorpion Clan serve as the Emperor's Underhand. They protect the Empire from hidden or subversive threats, the sort that can't be met with force of arms. Rokugan's CIA, basically. Sounds good, right? Well, the leader of the Scorpion Clan, Bayushi Shoju, discovers some hidden prophecies that foretell the return of the dark god Fu Leng ... at the hands of the last of the imperial Hantei line. So, Shoju does what any well-meaning defender of his homeland would do. He unseals the Bloodsword "Ambition" and uses it to kill the Emperor and his family, while his army seizes the Imperial City in what would later be known as the Scorpion Clan Coup. Of course, the Emperor's weak, borderline-retarded son manages to survive, and when the Coup is inevitably foiled he is installed on the throne with Shoju's widow as his wife, where she proceeds to poison and corrupt him for years until he's so weak that bad things start to happen.
 * Of course, with the rise of, he might have had the prophecy completely wrong anyway.
 * In the Battletech universe, during the Clan invasion, Clan Smoke Jaguar War Ships power up their weapons and glass a Draconis Combine colony world in an attempt to break the back of the stubborn Combine resistance. Not only did this serve to alienate their allies, drive the Combine to even greater heights of stubborn defense, but, when a defector revealed the Exodus road, the closely guarded secret route to the Clan homeworlds, the battle cry (and mission) of the armada of the Restored Star League Defense Force was "Clan Smoke Jaguar Must Die!"
 * Magic: The Gathering features Garruk, who was forced to join the army as a child. His father hid him instead, and he came back and killed the lord.
 * Inverted in Warhammer 40,000 of all places. When the Imperium first encountered the Tau, they were a race of non-technological primitives living on one world. They were scheduled for routine genocide (it's that kind of universe), but the paperwork got lost somewhere. A thousand years or so later, and the Tau are the fastest-growing alien empire on the Eastern Fringe, and a major thorn in the Imperium's side. Keep in mind the Tau never realized the Imperium even existed, much less had them slated for death.

Theatre

 * Excellent example in The Trojan War Will Not Take Place : Hector claims that the nation he fought was the most barbaric one, so there will no longer be wars because Trojans killed every child. Except one, because Trojans are not Complete Monster. Andromache answers that this child will have uncountable descendance, so in some centuries the world will be at total war.

Video Games

 * In Bastion, the Caelondian government
 * In Final Fantasy IV, the king of Baron tries to wipe out the Summoners. He does a pretty good job, but he misses one, the young summoner Rydia. However, it isn't played completely straight in that the backfire mainly came from the main character defecting to eventually take him down rather than Rydia herself.
 * In Final Fantasy IX, the summoners of Madain Sari are also wiped out by the Big Bad long before the game... except for Eiko and.
 * In Final Fantasy VI, Kefka poisons the populace of Doma, and one of the only survivors ends up being a player character who potentially takes him down. Kefka differs from most examples of this trope as he did it basically for the hell of it rather than some overarching goal of self-preservation.
 * The Old Republic, introduces a heroic version as part of the backstory; A large part of the Sith Empire's motivation is revenge after the Republic exterminated the rest of their society.
 * And in Knights of the Old Republic, One of the only people who escape the bombardment of Taris is the exact person Malak intended it to kill.
 * The Player Character in Jade Empire is the last surviving Spirit Monk, an order who were slaughtered so that the Emperor could steal the power of their goddess, the Water Dragon, to defy the Heavens and end a severe drought. Subverted in that
 * A bit of a stretch, but in Nethack, it is possible to get scrolls of genocide. So it is possible to use it to, say, wipe out all dwarves in the dungeon. Which kinda bites you in the ass if you happen to be a dwarf. With a little imagination and WMG you could play both the dastardly villain who wipes out the victim population, and the hero who valiantly gives his life to put an end to the monster who destroyed his people.
 * Not to mention what happens when you read a cursed scroll of genocide: Instead of wiping out the desired species, it summons a number of them instead. Genocide backfire indeed.
 * In Guild Wars: Prophecies, the White Mantle ritually identifies the Chosen and then sacrifices them to their gods; discovering this is what drives the Player Character to turn on the Mantle. Then the Player Character is revealed to also be Chosen...
 * The Lombaxes and Cragamites in Ratchet and Clank Future: Tools of Destruction. The Lombaxes sealed the Always Chaotic Evil Cragamites in Another Dimension, save for one Cragamite child they took pity on. This lone Cragamite, Emperor Percival Tachyon, then raised an army and wiped out the Lombaxes for daring to pity him. But he missed Ratchet, who proceeds to trap him in Another Dimension with the rest of his mad race.
 * Played with in the Metroid series. Metroid 2: Return of Samus has Samus tasked with exterminating the Metroids on their home planet of SR388; the game ends with Samus sparing a single hatchling, which has imprinted on her. Super Metroid starts off with scientists studying the larval Metroid making the discovery that the Metroids have abilities that could be used for the good of galactic civilization, right before the Space Pirates massacre the researchers and abduct the larva so they can build another Metroid army; the next time Samus encounters the larva, it's grown to horrendous proportions and almost kills Samus before it recognizes her. Then, during the final battle, it performs a truly heartbreaking Heroic Sacrifice, saving Samus from Mother Brain's onslaught and giving her the unstoppable Hyper Beam weapon. (Then Metroid Fusion reveals that the Metroids on SR388 were keeping an even more dangerous threat in check, which is another trope entirely...)
 * Samus herself is portrayed as the sole survivor of a Space Pirate attack on the mining colony of K-2L. Who would have thought that cute, 3-year-old girl would come back to bite them in the ass so hard.
 * Iosa the Invincible of Iji had her homeworld Alpha Struck by the Tasen. She didn't take that very well.
 * For that matter, Iji is one of two known human survivors of the Tasen Alpha Strike and subsequent invasion of Earth, and the other is playing Mission Control for her.
 * The Covenant failed to commit genocide on mankind in Halo. It started in 2525 when the High Prophets found out that the Humans were the inheritors to the Forerunners, the species that the Covenant worshiped as gods, and they realized that the truth about it would splinter the Covenant if it ever was spread. They decided to wipe out Humanity so that no one would find the truth. 30 years later, all the High Prophets were killed, the Elites became the Humans' best friends, High Charity fell to the Flood only to be destroyed by Master Chief, the Covenant lost billions of soldiers in the battles of Reach, Earth, the Halo and the Ark and the Covenant is now nothing but a shadow of its former self.
 * The big backfire was when they tried to genocide the Elites after they found out the truth about the rings. The Elites thus joined forces with the humans.
 * The new Forerunner Saga novels reveal that the Forerunners and the ancient human interstellar empire fought a devastating war, with the Forerunners winning and literally blasting humanity back to the Stone Age. Unfortunately for them, the humans had plenty of research and experience with the Flood, which was destroyed when Earth fell. Then the Forerunners themselves get wiped out by the Flood.
 * In Mass Effect, The Quarians try to do this to the Geth to defy AI Is a Crapshoot. To quote John Doe, it didn't work.
 * The third variant occurs in the Age of Empires III: The Warchiefs. Chayton Black has some moral reservations about killing women and children just to help the gold rush along, so he defects to the Sioux he was ordered to kill. This ends badly for Billy Holme.
 * A fairly straightforward case in Bayonetta: the Big Bad, the last Lumen Sage, began the Witch Hunts against the Umbra Witches (in which the titular heroine is a member of) more or less For the Evulz. Naturally, Bayonetta stops this plot.
 * In the Forgotten Sands variant for the PSP - there are four different games on different consoles under that title - an ifrit hears of a prophecy stating that a lonely hero with royal blood will kill him, so he starts assassinating people who are part of Persia's royal family. The Prince of Persia, upset over the deaths of his cousins, then tracks down and kills the ifrit. Self-Fulfilling Prophecy.
 * Metal Gear Solid 2 Sons of Liberty does a subverted variation: The Patriots had Dead Cell liquidated (IE, most of its members killed off) for terrorist attacks it apparently committed. In actuality, the Dead Cell unit was actually framed for the Terrorist activities by the Patriots (in other words, it was actually the Patriots who did terrorist attacks on its own country), and more importantly, they deliberately allowed some survivors to exist in Dead Cell specifically to get them angered enough to attempt to challenge them and more importantly further use them in the S3 plan.
 * In Dragon Quest II, Hargon kills everyone in Moonbrook, but turns the princess into a dog rather than kill her.
 * In Dragon Quest IV, the Hero's village is destroyed, but he's hidden away at the time.
 * In Supreme Commander a paranoid Earth Empire commander waged war with the Seraphim and their human followers, but they were easily defeated by their numbers and weapons, in their last ditch effort take them out they unleashed a bio weapon that only targets the Seraphim slowly killing them all. But what they killed was only a very small portion of the Seraphim race who live on the other side of the quantum realm, in Forged Alliance they cross into human realm and conduct their own genocide on the humans.
 * A variant occurs in God of War II. While Kratos is off on his quest to find the Sisters of Fate, Zeus decides to wipe out his beloved Sparta. One soldier (whom you met in the beginning of the game) survives the attempt and tries to seek out the Sisters himself.  This only serves to make Kratos even more pissed and hellbent on taking revenge on Zeus.
 * In the first Homeworld game, this is how the Taiidan Empire meets its end. After the main race perfect hyperspace technology, the Emperor (who is indisputably insane) decides to invoke a long forgotten, thousands-of-years-old treaty that the race had forgotten, which was that they were not allowed to develop any hyperspace technology. This results in the near-genocide of said race, and in addition to causing the survivors to get royally pissed off and begin a war against them, also results in a massive rebellion popping up due to public outrage of an essentially unprovoked attack on a fledgling race that had just started interstellar travel. By the end of the game, the main race is assaulting the Taiidan homeworld with the aid of the rebels, and destroys the defense fleet as well as the Emperor's flagship, then goes down and destroys the cloning facilities that housed replacements, destroying the Empire entirely except for a few remnants with little power.
 * In Dragon Age: Origins, during the Human Noble origin, Arl Howe attempts to wipe out the entire Cousland linewhen the main army leaves Castle Highever to fight the darkspawn. However, thanks to the Grey Warden Duncan, the player survives, becomes a Warden, gains armies of support and powerful allies, and eventually returns to Howe's manor to express your disapproval of his ambitions by rearranging his face.
 * Double Subverted in Mega Man ZX and its sequel, Mega Man ZX Advent. In a similar manner to the S3 Plan, Serpent (and ultimately Albert) were heavily implied to have deliberately spared only a handful of people during Maverick Raids in order to get them to become Mega Men and thus participate in the Game of Destiny to become the Mega Man King. However, by the end of the game, regardless of the deliberate attempt to spare them or not, it still put an end to their plans and presumably the Game of Destiny.
 * Genocide attempts has happened quite often in the history of the World of Warcraft, though only a few have backfired.

Web Comics

 * In Start of Darkness, crusading paladins go and wipe out multiple villages of goblins while seeking the high priest, whose God has a plan that threatens the very fabric of creation itself. In the process, they killed every man, woman and child they could find, but missed two -- Redcloak and his brother. In the current story arc, Azure City has been conquered by Redcloak and his armies, and is running the human population into the ground.
 * And in comic 842, boy does Darth V's Familicide coming back to bite him/her in the ass.
 * , all from It's Walky!, killed all the so-called "Martians" in The Seventies. "So-called" because . Of Cthulhu Mythos-like creatures who'd been leaving around all that sufficiently advanced Imported Alien Phlebotinum that drove half the comic's plots. This goes about as well as you'd expect.
 * Admittedly not a perfect example since (other than ) it went exactly as planned for the small subset of humanity that ultimately engineered it.
 * Sometime during the Dominion War in Terinu's past, the human rebels attempted to destroy the Varn Dominion's main power source. Said source consisting of childlike sentient beings known as the Ferin. The Terran Federation trying to both finish the job and keeping the secret from their allied races is a major plot point.
 * A few centuries into the back story of Errant Story, the Elves discovered that some Half-Elves may go crazy and spontaneously develop inexplicable talent in destructive magic. The Elves forbade cross-breeding with Humans and organized a branch of the military to hunt down Half-Elves. They haven't been exterminated-- there are at least enough Half-Elves to populate a hidden village-- and no prophecy is involved, but one Half-Elf has absorbed a comatose Elven deity and is leading an army of the descendants of the Elves' Human bodyguards to wipe out the last surviving Elven city.
 * Even better: The reason that there's just one Elven city left? They were so smugly arrogant, callous and intractable in their attempted genocide that basically every other power group (including their erstwhile allies and pawns) basically told them where they could shove it. Violently.

Western Animation

 * In Avatar: The Last Airbender, Firelord Sozin knew that after he left Roku to die, the Avatar would reincarnate amongst the Air Nomads. So, the Fire Nation managed to kill off the Air Nomads... except for the one kid they were aiming for. What's particularly sad is that Sozin basically jumps over the Moral Event Horizon for no reason, the kid would have probably been trapped in the ice for the hundred years anyways. Aang ends up stopping the Fire Nation later (though they did screw up the world and their own cultural morality pretty badly in those 100 years he was gone).
 * Another complicated invocation of the trope is the Fire Nation tradition of hunting and killing dragons to prove one's mettle as a Fire-bender (again started by Firelord Sozin) which apparently pushed the species into extinction in less than 100 years, with Sozin's grandson, Iroh, acclaimed for killing the last pair. When Zuko, Sozin's great-grandson and Iroh's nephew, needs to find the original method of Fire-bending, before it became corrupted by relying on anger, guess who the original Fire-Benders who might have been able to help him were?
 * Subverted in Drawn Together, where the last survivor of genocide meekly submits to the killer.

Religion

 * The Bible provides some examples:
 * In Egypt, Pharaoh commanded that all male Hebrew babies must be put to death. The lone escapee, Moses, got the Hebrews free and inflicted massive damage to the Egyptians.
 * And before that Pharaoh attempted to secretly have every male baby Hebrew killed at birth by a group of Hebrew Midwives... who decided they were having no part of it. (Lying to Pharaoh that the babies were born before they arrived to midwife the mothers)
 * Jesus Christ, there's...Jesus Christ. Herod could not kill all the Jewish boys who had been born under the star of Bethlehem because Jesus was in Egypt. And John the Baptist was in hiding in the wilderness with his mother. However, neither Jesus nor John ever actually did anything to Herod; he just died of old age a couple of years later, while they were still small children. Though his grandson, Herod, got killed by an angel for persecuting the early church a couple of decades later.