I charge you further to submit to me as soon as possible a general plan of the administrative material and financial measures necessary for carrying out the desired Final Solution of the Jewish Questionnote or "Endlösung den Judenfrage".
—Order from Hermann Goering to Reinhard Heydrich, July 31, 1941.
It must be the deliberate extermination of (or intent to exterminate) a demographic of one's own species (genocide) or another species of sentient beings (xenocide), whether it is successful or not.
It must be done to fix a perceived problemnote e.g. typically a belief in moral-spiritual contamination as a result of associating with those to be exterminated. Expect the targets to be thought of as vermin and/or a disease that must to be cleaned up to make life safe/good/healthy for the exterminators.. If not, that's just For the EvulzOmnicidal Maniac and/or stuff.
In the eyes of the exterminators, the existence of said demographic/species is a problem/'question'note Languages other than English do not always make a distinction between the two. . While there is a grey area where Final Solution and Utopia Justifies the Means can overlap, the former is not in itself a subtrope of the latter.
The Manga/Anime Naruto has the culling of the Uchiha Clan when they tried to pull off a coup d'etat. From the Unreliable Expositor Uchiha Madara, he claimed this was due to the "discrimination" against the Uchiha Clan (despite all logic) which the Uchiha Clan got tired of. To preserve the peace in the village, Itachi had to kill his whole clan. It turns out that "Uchiha Madara" is not Uchiha Madara at all, though his true identity is Obito Uchiha. In context its quite clear that Itachi, who was only 13 at the time, was manipulated into the massacre by the resident Well-Intentioned Extremist Danzo, who definitely viewed it as this trope and convinced Itachi of the same- Itachi has since grown up and realized it was a little extreme. On the other hand, it seems that Itachi really did think that Tobi was Uchiha Madara, or claimed to think that, and Tobi really did assist him in the massacre and the rebellion might really have happened- as of this writing, Sasuke is still trying to find out if Itachi lied to him, or was lied to himself / mistaken, and what really went on. The whole thing more or less started with the Kyuubi attack and the fear that a member of the Uchiha clan was behind it- Tobi was behind it and since he is not Uchiha Madara, it is very likely that he is indeed a member of the Uchiha clan so this fear was a case of Properly Paranoid.
He is an Uchiha. He's Obito Uchiha. The clan considered him an outcast and a failure, and he ended up killing most, if not all of them. It's rather ironic, really. While Konoha was right in the fact that a member of the Uchiha Clan did cause the Kyuubi attack, it was a member everyone thought was dead.
Also becomes even more justified when the Uchiha start being portrayed as Always Chaotic Evil during the story, with each revelation about them becoming worse and worse: they kill their best friends and siblings for power, they abuse their Reality Warping ability on each other in 'Izanagi Wars', during the Clan Wars adult Uchiha gain up on Senju child soldiers and kill them maliciously, and of course, the Big Bad of the series being Uchiha Obito makes the story seem to go out of its way to show that the Massacre was necessary. It even seemed that the founding of the village for the Uchiha in the end instead of becoming a lasting peace between them and the Senju, it became a five decade truce.
The Ishvalan Extermination Campaign in Fullmetal Alchemist. What started out as a relatively normal war soon escalated into a bloody massacre, designed to wipe out the indigenous population of Ishval. It was ultimately unsuccessful. The majority of adult characters are veterans of the campaign.
The massacre of Ohara in One Piece. The only way to silence the scholars of Ohara from revealing the truth of the Void Century was to Kill 'em All. This also extends to every man, woman, and child who lived on the island who wasn't a scholar. Just in case.
Frieza's Genocide of the Saiyans in Dragon Ball Z by blowing up Planet Vegeta, done because he feared one of them surpassing him in power and threatening his hold on the galaxy. Which is ultimately what happened: four Saiyans survived the genocide (eight if movies are counted as canon), he's utterly defeated by one of them, and killed by the half-Saiyan offspring of another.
Mobile Suit Gundam AGE has recently entered this territory. Not necessarily Vagan; their goal could be achieved without massacring all natives of the Earth Sphere. No, this is the intended goal of Flit Asuno, the first protagonist, for Vagan.
Gurren Lagann: The Anti-Spirals consider the eradication of Spirals justified. Their view: Spirals can tap into Spiral Energy, kind of like turning the key on a wind-up toy. The more Spiral Energy is tapped, the more the key is turned...until you overwind. Then all the spiral energy collapses in on itself, taking the entire universe with it in a Big Crunch. So the Anti-Spirals believe they are trying to save the universe. Why didn't they show up earlier? They only notice you when you get above a certain threshold. Then they get medieval on you.
Elfen Lied: Pretty much every Diclonii in the series has been abused by humans to the point where their biological survival instinct has fused with their psychosis, which insists that humans must be eradicated or they will eradicate Diclonii. Turns out that is absolutely correct. Once knowledge of Diclonii is widespread, all Diclonii babies are killed at birth until human scientists develop a vaccine capable of keeping them from being conceived at all, annihilating the species.
In the Strontium Dog arc "The Final Solution," The New Church publicly claims that they're moving the mutant population in Britain to new homes in another dimension where they can live in peace away from normal human beings. What they're really doing, however, is rounding up mutants from their ghettos and dumping them in a dimensional wasteland to be stranded and killed by an Eldritch Abomination, but they know that nobody would make much fuss if they make it sound like a peaceful relocation program.
ElfQuest: Siege at Blue Mountain: Part of Winnowill's plan involves killing the Wolfriders' immortal souls as well as their bodies. (Admittedly there are less than twenty Wolfriders, but they're still an entire race of elf-wolf hybrids.) She fails, naturally.
In the Supergirl story arc during John Byrne's run on the Superman titles in the late 1980s, the three escaped Phantom Zone criminals of the Pocket Universe terrorized its Earth when they were released, and though its Earth no longer had Superboy to protect them, its version of Lex Luthor had built up a resistance force powerful enough to keep the Phantom Zone villains at bay. Ultimately the villains decided humanity was too much trouble to rule over and thus killed everyone outside Lex Luthor's Smallville citadel by burning away the Earth's atmosphere through destabilizing its core. They were punished for their crimes by the mainstream DC Universe's Superman exposing them to the radiations of both Gold and Green Kryptonite.
In Supergod, Krishna was programmed with creepy nationalism - he's designed to protect "India" rather than "The people". And thus the genocide begins.
Termight Empire in Nemesis the Warlock slaughters all aliens they ecounter in order to take over their planets for themselves. And because they're bigots.
V for Vendetta has this since the British government was overthrown by Neo-Nazis; the final solution has mostly succeeded in its goal (of wiping out every non-white, non-Christian, LGBT and/or politically dissident person in Britain) by the time the novel takes place.
In the movie Thor, Loki attempts to use the Bifrost to destroy the frost giants, which for most of the movie had been portrayed as savage and violent. Thor stops him by destroying the Bifrost.
Thor: The Dark World featured Bor, Odin's father exterminating all of the Dark Elves to prevent them from destroying the multiverse. Odin only grinned about it when recounting the deed and justified it by the thousands of years of peace it brought about. Somewhat averted as many of the Dark Elves were killed by Malekith covering his own escape and surviving. Thor and a few humans completed this when Malekith tried destroying the multiverse again.
Conspiracy follows the detailed formulation and dissemination of the plan for the Final Solution.
In Stargate Continuum, the Goa'uld consider the human population of Earth to have grown beyond their control. After Qetesh takes over from Ba'al, they decide to remedy this by orbitally bombarding the planet and reducing it to a more "manageable" number by killing as many people as possible.
In Aliens, Ripley and later the Marines want to wipe out the Aliens entirely. This is well justified and not the excuse of a genocidal bigot, since the Aliens actually areAlways Chaotic Evil monsters (or the very least an omnicidal species adhering to a Blue and Orange Morality, a species that is heavily implied to be a genetically engineered bioweapon that is supposed to supplant any sentient lifeform in the area it infects). Burke objects to this plan, but not because he thinks they have no right to do so (as he claims at first), but because he wants to collect a live specimen for the Company's bioweapons division and reap a big profit.
The Hitchhiker's Guide to the Galaxy starts out with some amoral bureaucratic aliens destroying Earth and mankind along with it, simply to make room for a new interstellar highway. In some versions of the franchise, the highway is a cover story for the real reason.
Played with in The Illuminatus! Trilogy. The bad guys kill off entire nations for not agreeing with them — or as snacks for elder gods.
Left Behind Antichrist villain Nicolae Carpathia refers to the battle of Armageddon one year before it happens as "the final solution", obviously referring to dealing with the Jews in Israel.
Noah and the flood — Mankind misbehaves? Let's exterminate all life on the planet! (Except for one family and their pets.)
Sodom and Gomorrah — Mankind misbehaves? Let's exterminate all life in this small nation! (Except for one family — and maybe their pets, if they had any.)
Invasion of Canaan by Moses and the armies of the Hebrews? Exterminate everyone in Canaan! Again, treated like a good thing despite one of the peoples that Moses exterminated helped him after he fled Egypt initially! If the Old Testament is to be believed, the Israelites did this or something similar to the Hittites, the Girgashites, the Amorites, the Canaanites, the Perizzites, the Jebusites, the Hivites, the Midianites, and the Amalekites.
About 350 years later, God rejected Saul after Saul spared the Amalekite King and livestock, in fact.
However, the Gabaonites were spared after currying favor with the Israelites (albeit through deceit), and the Israelites even defended them when other kings marched to war against them. The prostitute Rahab and her family were also protected during the siege and fall of Jericho.
The Book of Judges also makes it clear that the Israelites didn't finish the job. In their complacence, the Israelites absorbed practices from the remaining unconquered kingdoms (religious and otherwise) that ran in stark contrast to what was prescribed by Jehovah God through Mosaic Law. In rejecting God's protection as a result, surrounding kingdoms repeatedly had their way with them until the Israelites came back to Jehovah and asked for His help, hence the rise of judges.
Played with in Jonathan Swift's Gullivers Travels: The protagonist discusses exterminating the (according to him, morally superior) horse people on the basis that they are too proud to be efficiently enslaved. However, he reaches the conclusion that it's better to just leave them alone.
In the Bolo series, A breakdown in relations between the Terran Concordiat and the Melconian Empire eventually leads to both sides trying to wipe each other out. They both almost succeed. Almost.
In Ender’s Game, the human high command's decision to destroy all the buggers certainly fits this trope, though Ender himself is not consciously aware of it.
In the first Safehold book, Off Armageddon Reef, Corrupt Church Grand Inquisitor Zaspahr Clyntahn suggests the Final Solution to the problem of the lacking orthodoxy of the Kingdom of Charis and its potential threat to the Church. It is referred to as such frequently after the attack's failure.
Harry Dresden does this to the Red Court by turning their own magic against them. The bloodline curse instantly kills the entire species, everywhere that they exist in the world. Like most heroic versions seemingly justified, there is not evidence that any of them were anything but totally evil. Of course, given that it was a spur of the moment thing, he didn't really predict the resulting vacuum of power that would result, nor how it would result in a world verging on Crapsack.
Timeline-191: Jefferson Pinkard and Ferdinand Koenig coin the eponymous phrase which fulfills Jake Featherston's goal of wiping out all blacks in the Confederate states: "Population Reduction".
The Ra'zac (who are a species of evil bird-bats that eat humans) in the Inheritance Cycle faced a dedicated campaign of genocide from the Riders. Eragon killed the remaining four members of the species in Brisingr.
David Weber is prone to recycling tropes and plotlines. In addition to the Bolo and Safehold examples above it comes up in his novelizations for Starfire. It was almost carried out against the Rigellians (and orbital weapon platforms are left in place to prevent them from ever advancing to a point where they might regain space-flight) and seriously attempted against the Bugs since there was no way to communicate and they treated other sentient species as food. The clincher was that sufficiently large casualties (such as wiping out a planetary population) disrupted their Hive Mind enough that their massive defense fleets could be mopped up without horrific casualties on the part of the allied fleets. Only problem was that they missed one world.
Animorphs, Megamorphs #2, In the Time of Dinosaurs: stuck in the past on Earth, the Animorphs let a sentient species known as the Mercora die (by sabotaging the weapon that'll destroy the asteroid thrown at them), because if they don't, the dinosaurs won't die off and humanity will never arise on Earth.
Likely the largest genocide ever imagined is at the conclusion of the Skylark of Space series. The protagonists have before tanagled with the "ameboid" Chlorans, who attack, enslave and exploit humans (but do not exterminate them). In the earlier encounter there was just one Chloran planet; the option of genocide (called explicitly by that name) was considered, but due to pleadings of "soft-hearted" women the milder option of sending the planet far away was taken. But when discovering a faraway galaxy with millions of Chloran planets, the protagonist Seaton decides that the Chlorans are "a cancer" and a danger to the entire universe, and that nothing would do but to kill every single one of them - empatically rejecting any other option. He and his arch-enemy turned ally Du Quesne proceed to do just that, causing all the Chloran suns to go nova. "The Chlorans died in their uncounted trillions. The greeny-yellow soup that served them for air boiled away. Their halogenous flesh was charred, baked and dessicated in the split-second of the passing of the front wave from each exploding double star, moments before their planets themselves started to seethe and boil. Many died unaware. Most died fighting. Most died in terrible, frantic effort to escape... But they all died." Immediately afterwards, Du Quesne - feeling not the slightest remorse at having just killed uncounted trillions of sentient beings and destroyed an entire galaxy, proposes to his long-cherished lady love and is thrilled to hear that she truly loves him.
In the Uplift series the Galactic civilization, despite ostensibly placing great value on sentient life in itself, tolerates and even encourages a great deal of genocide in practice. Sometimes it's correct according to Galactic laws; for example, the Bururalli species were completely destroyed after they somehow devolved, went collectively insane, and started killing everything that moved on their first unsupervised colony world. Other times, it's just a matter of a politically powerful race getting away with destroying any species they happen to dislike, as when the Jophur obliterate the g'Kek because of gambling debts. The Tandu species are Absolute Xenophobes who long to wipe out everybody else. Even with the Tandu and Jophur, the "moderate" political majority make no attempt to prevent genocide.
Ryan West's The Rise of the Saxons features the heroic Anglo-Saxons attempt to wipe out every last filthy subhuman Celt in Britain, including children. To say that this might be uncomfortable for many readers would be an understatement.
The Malwa do this or try to several times in Belisarius Series as fitting their evil status. Aside from Belisarius having a vision of them doing this to Constantinople if the Byzantine Empire is not prepared, this happens to the Indian city of Ranapur-by official decree, not just the normal shell shocked troops going crazy after a long siege. The Malwa also order this done to the Maratha, however they are a Proud Warrior Race and don't take kindly to this.
The Malwa are actually led by a robot sent from the future by Transhuman Aliens who wish to manipulate time for the extermination of every race that is not them.
Many if not most older works in the field of mythology include genocidal acts which aren't viewed as controversial in the slightest (quite the opposite, actually) - the Old Testament for example is ripe with these. Modern fantasy literature, on the other hand, which otherwise borrows heavily from mythology, tends to avert this by and large: Here the pursuit of genocidal intentions is commonly present as a field of the evil faction.
In the Star Trek: The Next Generation episode "The Survivors", a god-like alien who'd taken human form saw everyone on the colony where he was living killed by hostile aliens called the Husnock, after not using his powers against them because he's a pacifist. After he sees his human wife's dead body, he snaps and kills the Husnock. As he explains to Captain Picard, who mistakenly thinks the alien's sense of guilt is merely over his failure to save his wife, he didn't just kill the crew of the attacking Husnock ship. He killed all 50 billion of them.
"No, no, no, no, you don't understand the scope of my crime. I didn't kill just one Husnock, or a hundred, or a thousand. I killed them all. All Husnock, everywhere."
In Star Trek: Deep Space Nine, The Federation turns out to be hypocritical bastards by the introduction of "Section 31", an organization within Starfleet. Section 31 specializes in committing crime and passing Moral Event Horizons whenever it benefits The Federation. In the later seasons, an empire known as The Dominion declares war on The Federation because they fear that the humans will harm them if given the chance. Of course, Section 31 have the solution: Wipe out the species that rules the Dominion, exterminate every last one of their species through biological warfare. Captain Sisko is outraged by this plan, in spite of its indisputable strategic advantages and in spite of the fact that the Dominion had attacked them. To balance this out, in the Grand Finale, the Cardassians turn on their Dominion allies. What does the Dominion do? Orders their soldiers to carpet bomb the planet, with the goal of exterminating the Cardassian race. Luckily, they are persuaded to stop before this happens, ironically because Odo gives the Female Changeling the cure to Section 31's virus in exchange for ending the war. But not before they've killed over 800 million Cardassians.
In the episode "Waltz", Sisko pushes a mentally deteriorating and hallucinating Gul Dukat to admit that he really was a madman ruling the Bajorans with an iron fist by getting him to admit that he really did want to kill all the Bajorans.
The Borg and "Species 8472" are trying to do this to each other: It's a war, but their goal is to exterminate each other's populations rather than achieving some kind of victory where the enemy's people still exists. The whole thing started with The Borg trying to assimilate 8472, but the whole thing had already moved far past that point when Voyager showed up.
The episode "Remember", where B'Elanna Torres realizes that a group of Enarans were responsible for exterminating a group of people called the Regressives through "forced relocation".
There's a Show Within a Show example in "Living Witness", where an evil depiction of Janeway decides to exterminate an alien race by using biological weapons against their planet, killing close to a million people.
Continuing StarTrek's attachment to this trope; in Star Trek: Enterprise, the Xindi arc centers on a group of aliens who believe humanity will destroy them, and so, logically, they figure their only option to Final Solution them first. They managed to kill more than 7 million people during a test run; the completely prototype was to finish the job completely.
The Xindi are one of the few villains in Science Fiction who make every effort to ensure the final solution is indeed final. Captain Archer discovers a rogue group of Xindi are preparing a biological weapon to be used on Earth's past as a kind of backup plan should their Kill Sat fail. Additionally, one episode shows that though the Xindi destroy Earth, they actually go after every single colony and outpost, literally chasing humanity down to the ends of the galaxy.
In Firefly, the theme song line "burn the land and boil the sea" refers to what the alliance did to Mal's home planet.
This is the Cylons' objective towards the humans in bothincarnations of Battlestar Galactica. In the RDM version the humans attempt to do it right back to them when they discover a virus that is lethal to Cylons on an old space probe. They fail due to Helo's doing.
This is a recurring concept on Doctor Who. The obvious holders of the trope would be the Daleks- Absolute Xenophobes who want nothing but to wipe all life but themselves from the universe. The Doctor himself has attempted genocide against the Daleks on at least three occasions. (It never quite sticks.)
In Babylon 5, Edgar's anti-psi conspiracy edges into this when it's discovered they've developed a virus that will kill off active telepaths or make them addicted to a cure the conspiracy produces. Edgars himself arguably fails at the third point, as he views it as a piece of Dirty Business beyond compare and constructs himself as Necessarily Evil and trying to save humanity from the Psi Corps. It's a moot point either way as Psi Corps busts open the conspiracy and kills him.
Had the second season of Captain Power and the Soldiers of the Future been made, the Bio-Dread Empirenote which some see as a metaphor for Nazism would have shifted their focus from digitizing humanity to essentially this. Keep in mind that this is a family show that aired in weekly syndication.
Supernatural's Lucifer planned to exterminate all humans from the planet, along with all the demons.
Sliders: In "Prophets and Loss", an Evangelical Right so evil and powerful that it has outlawed all science and performs chemical lobotomies on "rationalists" claims to control an interdimensional portal to heaven. The heroes notice that it looks awfully similar to their own portal... but it doesn't actually go anywhere; it's just an incinerator tied to a special effect so that the church can vacuum up assets from the gullible and kill them. The Chief Oracle even describes herding unbelievers into these ovens as "the final solution." Take THAT, Jerry Falwell!
In the Stargate SG-1 episode - "The Other Side" - a race known as the Eurondans beg help in defeating a vicious enemy which started a war that devastated their world and reduced them to hiding underground. Turns out the war was started by their leader's father and that they plan a final solution to get rid of the innocent race they term 'breeders' and hate because they don't practice eugenics.
In Stargate genocide seems to be a pretty common option for ..the good guys. Notable victims of almost entire eradication include the Goa'uld, the Replicators (twice), and the Ori. The Goa'uld and Ori were both Always Chaotic Evil in the most literal possible sense, so killing them all really was the only option. The Replicators were more of a mixed bag, but even the more sympathetic and reasonable ones ended up dead. Oddly enough, the only recurring villains they haven't wiped out yet are the Wraith, for whom humans are the only possible food source.
GURPS Aliens features one race prone to genocide and one that constantly gets genocided by everyone else.
The former is a mad scientist race who take over planets and experiment on the population, then clean up their mess by killing everyone so there is no witnesses. Quite tidy.
The latter is a sentient virus. It is colonies of the virus that are sentient, so every infected human or animal counts as one intelligent "virus colony individual". In spite of it being sentient, most races treats this species as if it was a normal disease that should be cured. (And no, destroying the virus is not needed for getting possessed people back: the virus is capable of moving to animal hosts and blank clones.)
In Task Force Games' Starfire, the fanatically racist and warlike Rigelian Protectorate was completely wiped out at the end of the Third Interstellar War under the Alliance's "Genocide Decree".
In Warhammer40k, the Imperium have a simple way of dealing with planets of its own population when they are considered tainted beyond recovery: End all life on that planet. Oh, and they are pretty fond of exterminating sentient extraterrestrials as well when they get the chance to do some "purging".
This asubtle goal of the Orks. Being a race of Blood Knights they seek to fight all they see and eventually kill it.
On a larger scale the Necrons employ this trope both to feed their C'tan masters and permanently sever their universe from the warp.
This is no longer the case as of the 5th Edition update of the Necrons, which gave their backstory a complete overhaul.
According to a blurb from the 3rd Edition Eldar codex, this is their plan for us humans if their race ever get out of the rut they're in. Worth noting that back then, quite a few players got it into their heads that they were the "good guys" of the setting. So much for that.
"Our time will come again, Eldrad has promised us. Once more you upstart Mon-keigh [subject spits] shall kneel before our power! This time we will not be so lenient! We will exterminate you, every world, every vessel, every one of you! Eldrad has seen the stars stained red with your blood, and it pleases him! You think us weak, but we will be your doom, children of Earth."
Starcraft: A rare "good" (of the Honor Before Reason variety) example. Being Scary Dogmatic Aliens as they are, this is one of the qualities of the Protoss. They're known of "healing" planets infested by the Zerg by purifying them. This also comes as one of the side plots in Starcraft II, where the player has to decide whether to side with Dr. Ariel Hanson (resulting in the mission "Safe Haven" and Hanson's departure from the Raiders to settle in Haven) or Selendis (resulting in the mission "Haven's Fall" and Hanson being infected by the Zerg cure and being killed later by Raynor) while discussing what's the best course of action in the planet Haven, being the target of a Zerg infestation.
A typical evil version occurs in the backstory for the Terrans. The United Powers League of Earth decided to kill 400,000,000 people who didn't want to go along with their plans for a "perfect" world. 40,000 of these folks were sent off into space, eventually colonizing the Koprulu Sector.
The Rite of Annullment on Circles that are judged beyond the hope of saving can be seen as this in the hands of Well-Intentioned Extremist Templar commanders, such as with the case of the Circle in Kirkwall when Anders blew up the Chantry in Dragon Age II.
When you go to the Circle Tower in Origins, you quickly discover that the tower is infested with abominations, and that the Templars, quite to their commander's distaste, is just waiting for word from Denerim to initiate the Rite of Annulment. You can either save the mages from this fate, or save the Templars from waiting for a reply.
In Prototype, the Blackwatch final solution to the virus outbreak is called "Operation: Firebreak", which is essentially nuking whatever location it has infested.
In Batman: Arkham City, Hugo Strange's plan for Arkham City was to make the Final Solution the only solution. This was Emergency Protocol 10, a military countermeasure that bombards Arkham City with missile strikes until everyone- criminal or otherwise- is dead.
In the Mass Effect universe, the salarians ended an interstellar war with the rachni by enlisting the krogan in exterminating them. Then, when the krogan decided to use the advanced technology that the salarians had given them to wage their own war of conquest, the salarians designed the Genophage, which caused 99.9% of krogan offspring to die during gestation. Whether the latter action constituted genocide is heavily debated in-universe.
Before the Genophage, krogan reproduction was positively explosive. Their home planet was so harsh that a 99.9% fatality rate kept their reproduction in check. Once uplifted to the galactic community and in control of planets much much safer than their home, their rapid reproduction was quite worrying. The Genophage was introduced to keep their 99.9% fatality rate from their homeworld's extreme conditions intact regardless of where they settled. This is why the Genophage is still debated, and not just accepted as a clear-cut genocide.
Samus in Metroid Fusion crashes the Space station infected with X-Parasites into the parasites homeworld to eliminate all of the ones in the ship as well as the ones left in the planet.
Earlier in Metroid II, the federation decided to solve the problem of Metroids being used as biological weapons by sending Samus to their home planet in order to exterminate the entire species. This is what results in the population explosion of X-Parasites, because Metroids were originally genetically engineered by the Chozo to be their predator.
Kefka's poisoning of Doma definitely qualifies under this trope, and most likely his destruction of the world by rearranging the Warring Triad.
The Covenant in Halo attempts to do this to the humans, because the Prophets discovered that the humans were the descendants of the Forerunners, which completely discredits all of the major tenets of the Covenant's religion.
When the Covenant discovered the Hunters, one subspecies that consumed Forerunner metals was exterminated for the damage done to various artifacts on their planet.
In Suikoden V, Gizel attempts to create "a Falena for Falenans" by enacting this against the Beavers and residents of Raftfleet. Queen Arshtat also attempts this on two occasions: before the game's events against the people of Lordlake, and right before her death against the entirety of Falena. In both instances, she's being influenced by the Sun Rune.
In The Elder Scrolls the Norn wiped out the Falmer in Solstheim and nearly did the same in Skyrim. The survivors were taken in by the Dwemer who proved less than hospitable.
Vaarsuvius's partner and children are threatened by a vengeful dragon. Fueled by demonic and devilish magic, Vaarsuvius finds a solution to the problem: Vaarsuvius kills not only this dragon, but also any dragon that is in any way related to it — a quarter of the Black Dragon population — to stop the Cycle of Revenge. Zhe later learns that this included human descendants too and has a Heroic BSOD when zhe sees the extent of hir genocide.
While he currently doesn't have the power to carry it out, Redcloak has mentioned this as one of his alternative long-term plans: Exterminate the humans and maybe the Gods, too to make more room for his beloved goblinoids.
Done twice in Titan A.E.. First the Drej against the humans (which is rightly treated as villainous), then the humans against the Drej — and the latter act is treated as a happy ending.
It is implied somewhere that the reason the Drej wanted to kill all the terrans was exactly because of what the Titan was capable of doing to them.
It's also implied that this trope, and its counterpart, boil down to "If you commit genocide, it's perfectly okay for someone else to wipe you out." Or, "Genocide is okay if it's in self-defense. And kind of accidental."
A heroic example in American Dragon Jake Long. The Huntsman plans to kill every magical creature on the face of the Earth with the Aztec Crystal Skulls. After finding out that his former apprentice has betrayed him for a dragon, he gets her to rejoin his side by presenting her with a Sadistic Choice, only to be betrayed by her as she uses the skulls to kill him and the rest of the Huntsclan (herself included) instead.
The Air Nomads were wiped out in a massive genocide by the Fire Nation, a hundred years before the start of the show. Except they missed the one person they were aiming for.
The Grand Finale revolves around the attempt to repeat this with the Earth Kingdom.
In The Legend of Korra, the successor series to Avatar: The Last Airbender, the Big Bad wants to do a non lethal version of this by removing bending from everyone. It comes across as spiritual rape/mutilation in series and, given the abundance of Mundane Utility, he would have to start another world war. Not to mention it's unlikely the debending process removes the chance children of the debended can inherit bending abilities, just making things worse. Said Big Bad of the sequel series even calls himself "the solution".
Futurama plays this comically straight in "Into the Wild Green Yonder" when Leo Wong wipes out an entire species of leeches (save one) to make way for a parking lot. Nearly averted later in the movie when the reborn encyclopod reluctantly decides to preserve the DNA of its now-extinct archenemy race, the Dark Ones. Zoidberg eats the remains before the encyclopod can do this, however.
The Teen Titans get in on this trope with a race of spacefaring robots, on the grounds that said robots are bent on exterminating all organic lifeforms. Unfortunately, they do this on the word of a Fantastic Racist, who by the end of the episode, decides to consider humans worthless.
A Fantastic Racism form is seen in Alfred J. Kwak. To complete Dolf's resemblance to Adolf Hitler, he resolves to kill every mouse (mice have long been used as an analogy for the Jews, see Maus for instance) on the planet because they angered him.
The trope namer is obviously the real-life campaign of industrialized mass-murder against Jews, Roma, Soviet prisoners-of-war, homosexuals, the physically and mentally handicapped, and many other racial or political "undesirables" committed by the Nazis (and assisted by some of their allies) during World War II. Adolf Hitler used euphemistic language in his correspondences, calling it "die Endlösung der Judenfrage" ("the final solution to the Jewish question"). Hitler also notoriously referred to the conflict against the Soviet Union on the Eastern Front as "a war of annihilation", although the man who gave the actual order was Reinhard Heydrich.
The colonial army of Imperial Germany committed the first genocide of the 20th century against the Herero and Namaqua people in what is now Namibia. Overall, at least half of said populations were wiped out through mass executions, deliberate starvation and forced labor. Horrible medical experiments were carried out on children. Some researchers claim Hitler and his buddies were directly "inspired" by this genocide when deciding what to do with the "undesirables."
Gaius Julius Caesar allegedly did this to a Gallic tribe (note: not all of them), but it seems more probable that he only had most of their noblemen killed. Generally, he preferred diplomacy over genocide.
Also, naturally, all of the many attempted genocides that this century has witnessed, such as the Rwandan Genocide (radical Hutus murdering the Tutsis and any Hutu with a conscience), and the Armenian Genocide (Turks trying to kill all Armenians in their territory; don't talk about this in modern Turkey if you don't want to get arrested).
Romans did execute measures at least very close to this trope in their history. The populations of Corinth and Carthage (both in 146 BC) were massacred (in case of most fighting men) or taken as slaves (in case of most women and children) and the cities themselves were burned into the ground. This was about as close as it came to the spirit of the trope in the Roman Republic.
In the ancient period, the successful siege of a resisting city usually meant the extermination of the adult males and the enslavement of the women and children. (Bear in mind, this only happened if the city resisted and fought to the end. If the city surrendered, it would be subjected to far lighter treatment, proportionate to the length of the siege; a city that had surrendered as soon as the enemy showed up would usually be spared everything but the tiniest bit of looting, while a city that put up a fight for a while before giving up might expect to see a day or two of rape and pillage.)
The Mongols used this as a tactic: they would kill most of the people in the cities that fought them, leaving only enough survivors to spread the stories about their atrocities. This gave nearby cities serious incentive to surrender outright. Tamerlane, a prince of a Turkicized Mongol people and a Chinggisid by marriage, also engaged in scary exterminations (he shared the Mongol penchant for giant heaps of skulls).
When the Mongols entered Baghdad it was the jewel of the Islamic empire, crossroads of three continents, and renowned as a center of trade, culture, and learning. They didn't call it the Fertile Crescent to be ironic. Long story short, none of that still applies. In more detail: the Mongols depopulated the city so thoroughly it didn't recover it's 1258 population until the mid 1960s, destroyed the Grand Library until the Tigris river ran black with ink and red with blood, destroyed the millennia old irrigation network that made the Fertile Crescent fertile, and generally did everything they could to turn one of the most advanced cities on the planet into what we now think of Baghdad even 700 years later.
It is estimated that the Mongols exterminated 90% of Iran's population. For comparison Hitler killed less than 40% of Jews in Europe. In total they killed between 30 million and 60 million people at a time when the global population was around 400 million.
The ancient Assyrians used the same tactic as the Mongol example above — usually leaving extensive stelae with lurid descriptions of the shocking detail.
Many of the early wars between European settlers and the native North and South Americans came down to this; it wasn't uncommon for small settlements on both sides to be completely exterminated. King Philip's War is probably the best known of these, and probably the worst in terms of percentage of the population killed. And then of course there's the casual and systematic use of biological warfare, i.e. smallpox infected blankets.
Only later on. When Europeans and natives Americans first met, Europeans had no understanding of Germ Theory, and were just as confused by the sudden outbreak of disease amongst the natives they encountered. Early Euro-American dealings were a bit more egalitarian due to trade and religious motivation for earlier Europeans (native tribes could be converted and civilized, which can't happen under Eugenics). The outright cultural repression, assimilation, and killings started after the end of The War of 1812 (when British Canada and the United States were more secure in their territorial claims, and thus didn't need their native allies any more).
Subverted in terms of historiography: many scribes very deliberately exaggerated how much damage a war caused, often using such high numbers in their accounts that the opposing force would be practically exterminated, which would be at odds with the later wars that occurred.
When the Maori invaded the Chatham Islands, they systematically murdered at least 10% of the native Moriori population, some by torture, then enslaved the remaining people and prevented them from marrying or having children with each other. As if genocide needed to be any more horrific, the Moriori lived by a code of absolute non-violence and made no attempt to fight back.
During the National Reorganization Process, the Argentine military attempted what would be properly termed "politicide" against the nation's leftist elements, with the goal of a Final Solution to the Communist problem. Up to 30 000 people were killed, most of them guilty of nothing more than being more to the left than the hard-right junta.
This is what happened in the Yugoslavian wars. Every side tried to kill all the minorities in their territories, giving rise to the term "ethnic cleansing".