Dragon Ball Z: Frieza exterminated the Saiyan race in an attempt to prevent any from potentially becoming the legendary Super Saiyan. He missed four (excluding the ones from the movies which put it at eight or so). 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.
Vegeta even Lamp Shades this shortly before Frieza transforms into his second form.
Vegeta: So, you tried to eliminate the Saiyans, yet you left the strongest one alive! Smooth move!
Frieza's plan was to more or less keep the survivor Saiyan under his thumb and under close watch so if any of them rebel he could easily kill them. It works to an extent since he does kills Vegeta easily after his rebelling. The Ginyu Force would had wiped out Vegeta sooner if Goku did not interfere. Frieza's biggest mistake was not accounting for all the remaining Saiyans, namely Goku. He even lampshades this himself to Zarbon when he got a feeling that a Saiyan was coming to challenge him and it was not Vegeta who he feared, which is why he sent for the Ginyu Force to begin with.
In Hunter × 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 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 subvertingInfant 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 Itachi with the Uchiha Massacre. He leaves Sasuke alive because he wants to die by his hand. It still falls through, though; by this time, Sasuke has abandoned the Leaf Village, and afterward, he decides to actively destroy it.
Danzo was concerned about this himself. This is why he felt that, during the Uchiha massacre, it was necessary to even kill off everyone, even children. Considering that the one survivor now wants to destroy the village, and eventually killed Danzo himself, he may have had a point. Then again, Danzo's actions in the name of Konoha have oftentimes created even worse problems, so this probably came from experience.
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 (Ishval was chosen simply for its location) - 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. Later, he does a Heel-Face Turn and starts helping the Elric brothers. In the end, he plays a crucial role in causing the Big Bad's Evil Plan to fail and kills Bradley, the man who ordered the genocide - which he would not have done, if the genocide had not existed in the first place.
In the 2003 anime version, the purpose was to make the Ishvalans desperate enough to attempt to create a Philosopher's Stone — something Scar ends up doing by using an entire army unit of Amestris as the resources for one. Meanwhile, Bradley is killed by one of the soldiers who was a part of the Genocide and was instilled with an immense hatred of the current system by the atrocities committed there — Roy Mustang.
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 Bakura.
In the Yu-Gi-Oh! GX manga, it turns out to be responsible for that series' Big Bad, who was from said village as well, and was understandably pissed-off when it turned out everyone he knew had been horrifically murdered, and tried to kill the pharaoh. It didn't work, and gets him sealed away until he's released some time after the events of the original series.
Bleach: Soul Reapers cleanse Hollow souls back into the reincarnation cycle while Quincies destroy the soul completely, damaging the Balance of Souls between worlds. To save existence itself, the Soul Reapers wiped out the Quincies but didn't know until too late that most Quincies were in hiding, building their power to retaliate. Only a very few on both sides suspect the two sides are equally to blame.
In One Piece, the World Government was worried that the scholars of Ohara would discover the Void Century, a point in time they didn't want anyone to know about. Therefore, they exterminated the entire island. The lone survivor, Nico Robin, vowed revenge by discovering the Void Century.
In one Lanfeust spinoff, an alien shapeshifter race is genocided due to their aggressive attacks on many planets. Only one individual survives, but eventually hatches a plot to control the Galaxy and causes much destruction.
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 existence 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.
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 has no idea what he'd done. Further played with at the very end where the audience learns that the village re-settled elsewhere, so it didn't just backfire — it straight-up failed. Nonetheless, Shen's actions were what facilitated his defeat, as it would eventually cause the baby Po to end up in the Valley of Peace, which would allow him to get the training he would need to defeat Shen.
In Titan A.E., the Drej destroy earth reducing humanity to a few thousand scattered survivors because they believed us a threat. In the end the Drej are used to power the Titan and create a new homeworld for the human race.
Films — Live-Action
Avatar: The RDA Security Force, under Colonel Miles Quaritch unleashed missiles on the Hometree, killing nearly every Na’Vi, including Princess Neytiri’s Father.
It did not have the effect Colonel Quaritch had planned.
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.
Funny thing is, Riddick doesn't give a shit about any prophecy and only wants revenge for himself and a few others he might call friends.
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 a double invoking of the trope, the male Gelfling Jen is saved by one of the old Mystics and raised among them; on his deathbed, the eldest Mystic sets Jen on his course to defeating the Skeksis. Meanwhile, the female Gelfling Kira is hidden by her mother just before the Garthim take her, and is found and raised by the Podlings. The Skeksis-serving Garthim still raid the Podling villages, to boot.
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.
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.
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.
In TRON: Legacy, Clu kills off all the ISOs, emergent programs that Kevin sees as a miracle but Clu sees as "imperfect". By the end of the movie, Clu wants to exit the Grid in the worst way, but he gets re-merged with Kevin while Quorra, the last ISO, rescued by Kevin, escapes the grid to the real world with Kevin's son Sam. Not quite a genocide backfire since Quorra didn't land the fatal blow, but Quorra got to leave the Grid while Clu did not.
The Godfather 2 The local ganglord kills Vito Andolini's father, then his brother when the brother tries to get revenge, then his mother when she tries to protect Vito ('because he's slow'). Vito then has to leave Sicily for America, where he becomes Vito Corleone. He then returns to Sicily to off the ganglord.
Arguably happens in Dune, where the Baron Harkonnen kills his rival, Duke Atreides, and attempts to do the same with his only son, thus wiping out the Atreides family line and ending the millennia old Atreides/Harkonnen blood feud. At first he thinks he's successful, but they never find the boy's body...
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 discouragecompetition, now. And it would be a waste of people to kill everyone.
Ironically, even this fails. One of the recruitable characters in the Baldur's Gate series is one of the few surviving members of this family.
Then again, she is a non-Lloth priest, so she may have left Menzoberranzan before.
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. His descendants were free to live without being troubled, provided they never 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. He was vain enough that he always left the one descendant who looked the most like him alive. Of course, this bit him in the ass when the survivor of the last generation played a key role in the Patriarch's scheme to destroy him.
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.
On the positive side of things for the Achuultani, due to certain plot developments and revelations, it is quite likely the eventual human counter-attack will include willing Achuultani participants seeking to free their fellows from the AI that has effectively enslaved them via the cycle of near-genocides and a liberal definition of crisis.
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.
The Belgariad: the line of Riva was supposedly killed off by Queen Salmissra. One prince survived, and his descendants were hidden by Polgara and Belgarath.
Lord of the Rings: Sauron believed that he had killed off the line of Isildur. He forgot about Aragorn.
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.
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).
A rare heroic example: The Doctor has attempted genocide on the Daleks at least four times. It never takes. They just hate him even more now than they did before.
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. Not only is he his (other) arch-enemy, but the rest of the Time Lords use him to escape.
The Doctor ended the Time War through the use of some unspecified superweapon, which was supposed to kill all the Daleks and accidentally killed all the Time Lords, but Daleks keep popping up. It becomes clear in the Tenth Doctor's last episode, however, that this is because he wasn't just aiming at the Daleks.
In the 50th anniversary special, it's revealed that rather than destroy the Daleks and the Time Lords the superweapon in question convinced the Doctor, with help from two of his next incarnations, to hide Gallifrey in a pocket dimension. Ultimately, it would have been the Daleks aiming at themselves.
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.
In Lexx His Divine Shadow was very thorough in wiping out the Brunnen-G, but he made the mistake of reanimating the last one. The Divine Shadow himself is the parasitic essence of the last Insect that the Brunnen-G missed when they defeated the Insect Civilization.
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.
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.
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 real backfire that happened was that one of the races that helped destroy their empire in the first place also introduced some disease treatment whose absence 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. Ultimately, the problem is solved when Voyager rams the superweapon when it's about to fire, causing it to Ret Goneitself.
Uther Pendragon in Merlin attempted to kill all the magic users and dragons he could find. Now that he's cleared out all the harmless, innocent ones, the more violent and powerful ones are gunning for his blood. He did manage to kill all the dragons, but decided to keep the last one as an example. When it gets loose, it very nearly burns his city to the ground. And just when you think he's too much of a Karma Houdini his daughter Morgana turns out to be magical and kills him.
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.
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.
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.
In the Battletech universe, during the Clan invasion, Clan Smoke Jaguar WarShips 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!"
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 Daigotsu, he might have had the prophecy completely wrong anyway.
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.
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 the Trojans killed every child. Except one. Andromache answers that this child will have uncountable descendants, so in some centuries the world will be at total war.
In Bastion, the Caelondian government had the Calamity created in order to completely eradicate the Ura to prevent them from ever having to go to war again. When he finds out, the Ura scientist that created the Calamity sabotages it so that it destroys the world instead.
In Final Fantasy IV, the king of Baron (Actually Cagnazzo, archfiend of Water, in disguise) 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 Garnet, whose mother whisked her away to Alexandria.
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, Bastilla, one of the few people who escaped the bombardment of Taris, is the exact person Malak intended to kill when launching the planet wide attack.
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. The player character survives because of Master Li's plan and Master Li manipulates him into killing the Emperor for him so that Li can steal both the throne and the Water Dragon's power. In one ending, it works.
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.
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 heartbreakingHeroic 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?
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.
It goes even further. The Forerunners themselves had Recursive Precursors, who they called...The Precursors. The Precursors created both the ancient human empire and the Forerunners, but decided the Forerunners were a mistake and tried to wipe them out. However, the Forerunners struck first, and wiped out the Precursors. Then the Precursor corpses laying around broke down into a dust, which, thousands of years later, would become the Flood!
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 BadFather Balder, 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 Metal Gear Solid 2, the Patriots deliberately invoked this when they 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 committed terrorist attacks on their 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 IV, the Hero's village is destroyed by the Big Bad's minions, but he's hidden away at the time. Naturally, the Hero was the only person in the village that the Big Bad actually gave a damn about.
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. You end up fighting and killing the poor guy, but not before he tells you what happened to Sparta. 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.
The backstory reveals that this is how the original Hiigaran Empire fell. They were on fairly even terms with the rival Taiidani, until the Hiigarans got their hands on one of the Great Hyperspace Cores, allowing them to jump whole fleets enormous distances with pinpoint accuracy. They use it to jump their fleet into orbit of the original Taiidani homeworld and lay waste to it before jumping back. Outraged, the Bentusi and the other races demand that the Hiigarans surrender the Core, as they clearly abuse its power. Instead of peacefully handing over the Core, the Hiigaran fleet attacks the Bentusi, who promptly wipe out the whole fleet. As a result, the Hiigarans are now defenseless against the pissed-off Taiidani, who are now in need of a new homeworld. Cue the Curb-Stomp Battle and the exile of the Hiigarans.
In Dragon Age: Origins, during the Human Noble origin, Arl Howe attempts to wipe out the entire Cousland line when 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.
In other origins, the latter still happens but for a different reason. It's briefly mentioned that the entire Cousland line was wiped out in this case, though.
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 Worldof Warcraft, though only a few have backfired.
One that did backfired was the attempted genocide that the Mogu tried on their Servant Race the Saurok. To elaborate, after their conquest of Pandaria, the Mogu created the Saurok to police the enslaved races. Soon enough the Saurok realized that the Mogu had no way to control them, since they were given free will and fighting prowess in both sword and sorcery, so a few of their legions rebelled against their Mogu officers. This caused the Mogu emperor to decree the ethnic cleansing of the Saurok race. However 2 Saurok legions were stationed in the Mantid lands at the time, and managed to hide there despite the Mogu sending many armies of slaves after them, arguably since the Mantid were not too happy of having the Mogu invading their territory. Even worse, when the succesor of the Mogu emperor moved his palace to the Krassarang Wilds to oversee the genocide of the Saurok, the surviving legions took him by surprise and threw him off a cliff.Never succeeded indeed.
Sine Mora: Enkies are the mass-victims of Fantastic Racism. Enkies are also vital to psychic time travel. The empire (unadmittedly) runs on time travel. DO THE MATH.
In the backstory of Hatoful Boyfriend a version of the bird flu becomes so virulent that in two years seventy percent of humanity dies and there's no sign of stopping. In desperation humans created a virus of their own, an "avian annihilation" virus that would kill all birds. It kills many, but in the resistant ones there is another effect and the birds become uplifted, and immediately go to war on humanity. Thirty years later less than five percent of the human population remains and signs a treaty of surrender, and the world belongs to birds.
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, while it doesn't fall under any of the variants mentioned in the main article since it does wipe out everyone V wanted dead, boy does Darth V's Familicide coming back to bite him/her in the ass. The Draketooth family were all part dragon, namely, part of the same family V used Familicide on.
The reason the paladins of the Sapphire Guard chose genocide as their solution rather than simply hunting down the goblin high priest is that the high priest wears a magical artifact, the Crimson Mantle, linking his mind to the goblins' evil god the Dark One. If the high priest is killed, any other goblin can wear the Crimson Mantle and become the new high priest. Thus, the only way to end the threat forever would be to exterminate every last goblin in the world. (Destroying a divine artifact isn't really something within the power of mortals after all.) Now guess what Redcloak's new name (adopted several years after the genocide of his village) refers to.
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 worse: The half-elves learned absolutely nothing from this and tried to commit genocide on the elves in return, thus justifying the elves' genocidal rampage by the end of the war. Millennia later, some of the elves' erstwhile allies and some of the remaining half-elves STILL want to kill off all the elves. This ends about as well for said people as one might imagine, though the elves are less than happy with their rescuers. Probably because the elves are STILL the same genocidal jerks who caused the war in the first place, being immortal and all.
Fire Lord 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. 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 Fire Lord 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? He ends up finding the last pair, whom Iroh had lied about killing to protect, and is judged worthy of the knowledge he seeks.
Subverted in Drawn Together, where the last survivor of genocide meekly submits to the killer.
In the Book of Exodus, Pharaoh commanded that all male Hebrew babies must be put to death. The lone escapee, Moses, became the freer of the Hebrews. Worst of all, the Egyptians got the infanticide reversed on them when the tenth plague struck down all their firstborn.
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. (Specifically, he died of chronic kidney disease and Fournier gangrene, the latter of which is often interpreted as Jesus' dad invoking this trope.) Though his grandson, Herod, got killed by an angel for persecuting the early church a couple of decades later.