Genocide Dilemma

"The Doctor: Do I have the right? Simply touch one wire against the other, and that's it. The Daleks cease to exist. Hundreds of millions of people, thousands of generations can live without fear... in peace, and never even know the word "Dalek". Sarah Jane: Then why wait? If it was a disease or some sort of bacteria you were destroying, you wouldn't hesitate! The Doctor: But if I kill... wipe out a whole intelligent life form, then I become like them. I'd be no better than the Daleks."

- Doctor Who, "Genesis of the Daleks"

We all know the drill. It's The Federation versus The Empire, and the Heroes stop the Empire's new superweapon just in time for The Cavalry to defeat the Mooks. Now good has triumphed, how do you mop up the resistance? If the heroes are lucky, the Empire will be led by a Self-Disposing Villain or an Evil Overlord with a 0% Approval Rating who can be imprisoned in the Tailor-Made Prison.

But what if the driving force behind the forces of evil is not a single Evil Overlord, but a Planet of Hats whose hat happens to be Always Chaotic Evil? You can't very well arrest and try every inhabitant. And it will doubtlessly include children, who, if you did try them, would be acquitted because Children Are Innocent. But as long as enough remain to propagate the species, they will remain a threat.

Alice suddenly remembers that she still has the Handy Remote Control of that Wave Motion Gun her buddies just captured. The only question is, will the victors choose to use it and end the threat to the galaxy once and for all, running the risk of crossing the Moral Event Horizon themselves (although they and their allies might be reluctant to admit it), or be merciful and decide it's time for peace, even if that means they must risk the lives of their own descendants?

If the Always Chaotic Evil race is permitted to survive, it's a crapshoot whether they do a Heel Face Turn and become valued, if not always reliable, allies, or rise again to repeat the story in a sequel, possibly wiping out millions of Space Amish and other innocents in the process. If the Always Chaotic Evil race is exterminated, it's common either for one or a few to survive and become the underdog, resulting in a Genocide Backfire, or else that the Karmic effects doom The Federation to become The Atoner, or a Complete Monster in the eyes of history.

Occasionally, some other villain may conveniently exterminate the threat, who then has far less problems associated with killing him off.

In the modern world, killing enemies other than in the heat of combat or after a trial is considered a war crime, and animals and plants are protected by law in most places from deliberate extinction, but in the past this was not the case. Obviously, any serious discussion of genocide in the modern world is likely to run afoul of Godwin's Law, but keep in mind that for the Nazi leadership, there was never really an actual dilemma.

See also Final Solution and this trope's supertrope, He Who Fights Monsters. Contrast Would Be Rude to Say Genocide. When the characters don't show this at all during a war, it might be a Guilt-Free Extermination War.

Anime & Manga

 * The Saiyans from Dragonball Z presented this. There's
 * A major plot point in Elfen Lied.
 * Towards the end of Darker Than Black, the main character is faced with a choice, either let his enemies initiate a plan that would wipe out every contractor in existence, or stop them at the cost of wiping Japan (and presumably all it's inhabitants) off the map, literally. He doesn't want either to happen, but saving one would mean genocide for the other.
 * Trigun. "To save the butterflies, you must kill the spiders." But if you kill the spiders, you become a spider yourself...
 * The reason Zebra was imprisoned in Toriko. The 26 species he wiped out were damaging the ecosystem...but he's still responsible for making 26 species extinct.

Comic books

 * Secret Invasion: A What if... one-shot made a variant: the shape-shifting aliens Skrulls successfully invaded earth. They rule countries, live among humans, and even allowed humans to become skrulls. The Avengers, now a terrorist outlaw band, got a sample of the Legacy Virus adapted against the Skrulls. They face the dilemma: waste precious time trying to turn it into a vaccine, reverting the change in humans and removing the shape-shifting powers from the skrulls, or simply use the virus as it is and kill them all.

Film
"Ripley: "Just tell me one thing, Burke. You're going out there to destroy them, right? Not to study. Not to bring back. But to wipe them out." Burke: "That's the plan. You have my word on it." Ripley: "All right, I'm in.""
 * In the Alien franchise, somebody always seems to want to capture a live xenomorph....
 * But only to try to make them into a weapon. Lampshaded in the Green Lantern Alien crossover, Hal points out that the xenomorphs are just animals, so they move the hive to Lantern Mogo (a living planet) since he can watch them and make sure no one runs into one.
 * For understandable reasons, Ripley seems to have no moral reservations on this point:


 * The great irony with the Xenomorphs is that they need live hosts in order to spread. One person = one Xenomorph. If people would just leave them alone they wouldn't be a threat.
 * The third film establishes that they can implant other mammals.
 * In Titan A.E., some aliens apparently see humans this way. The story begins with one race making the decision to choose the 'better safe than sorry' route, which is why AE stands for After Earth. Of course, it doesn't work out as planned.

Literature

 * Keith Laumer's novel The Glory Game. After the warlike alien Hukk are defeated, the Terran Hardliners want to wipe them out to keep them from threatening Earth again.
 * Ender's Game and its sequels apply this in one way or another to every nonhuman species in the setting.
 * The Taxxons in Animorphs are driven by unceasing hunger, to the point that if one of them is injured, the others will eat its entrails. They voluntarily joined up with the resident mind-controlling parasites in the (unsuccessful) hopes that this would keep them from killing everything in sight. The issue of whether they need to die.
 * A variant: the Hork-Bajir are a peaceful species, but to weaken them as a tool for the Yeerks Alloran decided to genocide them with a Quantum Virus, earning a What the Hell, Hero? from his own species.
 * The Star Wars New Jedi Order series has the Alpha Red virus, which could kill the Yuuzhan Vong and their biotech, but Vergere destroys it because even the Vong have the right to exist, and the good guys would be monsters if they wiped them out. Or maybe she didn't have complex and noble motives, she was just an evil Sith villain. And then they recreate it, but it doesn't go too well.
 * Before the Vong, there were the Yevetha, whom Leia wanted to strand on their homeworld and set up an interdiction field for about the next million years. After the Vong, we have the Lost Tribe of the Sith, where Ben even says it's not genocide, it's just destroying the Sith. Light Is Not Good indeed.
 * In Andre Norton's BeastMaster cycle, this dilemma is resolved non-genocidally. Humans have defeated a race of Xiks. Xiks are clearly Always Chaotic Evil, but they're only left reduced to their homeworld and closely watched. When Xik spies' actions are revealed to be the cause of a series of disasters, they're hit with civil - legal - action, instead of military.
 * In the last book of Anne McCaffrey's Tower and The Hive series, humans and Mrdini debate whether it is moral to simply nuke the Hivers out of existence. Eventually, a Deus Ex Machina allows them to end the threat without wiping out the entire species.
 * In The Bible, the Old Testament Hebrews are instructed on various occasions to wipe an enemy nation to the last man, woman and child. The Israelites sometimes refuse, which comes back to bite them in the ass later. It's... a touchy subject.
 * L. E. Modesitt Jr. is rather fond of ending his books with this, and the heroes usually end up deciding to Shoot the Dog.
 * E. E. "Doc" Smith's Skylark series ended with Skylark DuQuesne, where Seaton was debating whether he should or even could wipe out the Chlorans. Eventually after much angst he decided to do it, but during the battle he was incapacitated, and DuQuense (who was the main villain through the series, and who had always sworn to kill Seaton if he had the chance) had to take over to finish the job on the Chlorans. He did so without a qualm, and "The man who slew a galaxy looked no different after the deed than he had before".
 * Stewart Cowley's Terran Trade Authority universe features the Laguna Wars - a nasty fight between Earth and mutinous humans who wiped out an alien civilisation centuries before and took over its machines. The adventure is written for children under ten but pulls no punches, especially near the end; when it's discovered that the cargoes the Earth forces were blockading (and which led the Lagunans to mount an ultimately unsuccessful last-ditch attack on Earth) were an antitoxin against a fungal disease in Laguna Nine's atmosphere. The occupation forces arrive to find to their horror that the entire planet has been completely depopulated. It's not total genocide - the industrial centre on Laguna Seven is still intact - but it's bad enough, and all the more horrifying for it being unintentional.
 * Subverted in Mike Resnick's book Birthright: The Book of Man. The other 13,042 sentient races in the Galaxy seem to have no moral qualms whatsoever about hunting Humanity to extinction. It's averted only by the fact that Humanity's last survivors - One man and three women - decide to go out with a bang (literally - they commit suicide by blowing up the planet they're on)rather than surrender and be executed. Same result though, I guess.
 * Subverted in Mike Resnick's book Birthright: The Book of Man. The other 13,042 sentient races in the Galaxy seem to have no moral qualms whatsoever about hunting Humanity to extinction. It's averted only by the fact that Humanity's last survivors - One man and three women - decide to go out with a bang (literally - they commit suicide by blowing up the planet they're on)rather than surrender and be executed. Same result though, I guess.

Live-Action TV

 * Babylon 5:
 * The writers took the easy way out of the Dilgar question by having their sun go nova shortly after the Dilgar War. How convenient. However, the original punishment was that they stranded all the Dilgar on their homeworld without Faster Than Light travel. The RPG tells of a Dilgar colony that avoided their fate, who (justifiably) stay out of galactic politics, but are not known for the horrors of the rest of the species.
 * Gets a bit more interesting, however, when it's pointed out the REASON Dilgar went to war was because their sun was going to go supernova.
 * The Minbari view Humans this way during the Human - Minbari war.
 * Battlestar Galactica: humans from a Cylon point of view. At the end of the Miniseries, the Cylons agree that they unfortunately can't give up pursuit of the human fleet even though it's left the Colonial solar system behind and just wants to get as far away as possible, because any survivors will inevitably return and seek revenge.
 * A more straight example: In the episode "Torn", the Colonial fleet discovers a virus that kills Cylons horribly and doesn't affect humans. Cue big debate about the ethics of intentionally infecting the Cylon Resurrection Ship with it. Despite the inevitability that the Cylons would have found a cure/treatment/ray gun that addressed the disease before being wiped out entirely (given their technological levels), the debate almost immediately leads to a member of the crew taking matters into their own hands to save the Cylons from the minor inconvenience of losing one resurrection ship (read: perceived genocide).
 * Star Trek. Klingons in The Undiscovered Country were a unique situation. An environmental disaster caused critical damage to their homeworld, which would almost certainly kill billions over the next several decades and probably plunge the Empire into a civil war. All The Federation had to do was sit back and "Let them die," as Kirk said. Instead the two governments decide to talk peace and mutual disarmament.
 * The third season of Star Trek Enterprise, with the Xindi being convinced by an alien race that humanity would destroy them in the future, so they tried to avert this by creating a xenocidal weapon. Although the debates tended to center around whether the accusation was true, and although the inventor of the weapon has his doubts on the morality, averting their own genocide is all the justification the Xindi need to Kill All Humans. An alternate timeline shows them tracking down human colonies even after Earth has been destroyed. Eventually, the Xindi factions are divided on whether to go through with the plan.
 * Star Trek the Next Generation: Picard is faced with the option to implant an impossible problem into the Borg's consciousness through a recovered drone. This would cause the entire collective to spiral out of control trying to solve it, and ending them. However, the drone, named Hugh, has developed a sense of identity. Picard ultimately decides to release Hugh back, hoping the spark of individuality will spread through out the Borg.
 * Picard's choice pays off for a few hundred of them, but then Data's Evil Twin Lore takes command of them, as seen in the "Descent" two-parter.
 * In Star Trek Deep Space Nine,  infects Changelings, leaders of the Dominion, with a virus that kills them - and because of their lifestyle, all Changelings are affected. The Federation discovers the cure, but refuses to hand it to the Dominion.
 * The Dominion itself, when presented with this situation 200 years ago (with the Ecorians), decided to Take a Third Option: they infected everyone on a planet with a disease that doesn't kill everybody at once, but rather is hereditary, incurable and can kill the host at any random time. 200 years later, the Ecorians still haven't even attempted to rebuild their society.
 * Stargate SG-1:
 * In an alternate history, O'Neill had never met Teal'c, and as a result, Stargate Command attacked his homeworld for this reason.
 * Subverted in Season Five, again with O'Neill. Subverted in that he only threatened it, and that he most likely didn't consider the sentient computer virus that had taken over his Second in Command to actually be 'people.'
 * The page quote from Doctor Who, where the Doctor doesn't want to wipe out the Daleks for fear of being no better than they are. He offers pitiful defences such as how the existance of the Daleks caused otherwise-disparate races to form alliances and friendships, but it's pretty hollow. He's saved at the last miunte from having to make the decision.
 * Over the course of the revival, as details of the Time War come to light, we learn that the Doctor was faced with a similar decision and he went through with it, wiping out the entire Dalek race and all the Time Lords in order to bring an end to the war. Coping with what he had to do is a big part of his character arc over the first four and a half series.

Tabletop Games

 * 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". The Alliance believed that all Rigelians everywhere had been slain until two planets were found with Rigelian survivors at a low tech level, leading to a quandary about what to do about them.
 * Magic: The Gathering's Phyrexians have this to some extent. While there are a few good ones, and the entire red Phyrexian faction of the last block is the Token Good Teammate of them (because asking a Vulshok or a goblin if he wants to take part in the Great Work is likely to result in missing a few parts), as long as a drop of Phyrexian oil exists, the Great Work can begin anew.

Videogames

 * In Mass Effect, The Rachni are a sentient, if extremely alien, species of insectoids who were thought to be actually extinct; you have the choice of either . A harder choice than it may seem, since the Rachni went near-extinct due to them embarking on a war with the Citadel Races, causing significant loss of life,
 * In keeping with the trope, you'll have some characters arguing that you can't justify destroying an entire species no matter how how much damage it once caused (keeping in mind that the Rachni Wars happened almost 2,000 years ago), and others who argue that it's time to "finish the job".
 * In fact, ; if you However, if you don't save her in the first game,
 * Another example from Mass Effect, but somewhat inverted:
 * In Mass Effect 3, at the end of the Rannoch arc, you get a choice between
 * In Mass Effect 3,
 * In Mass Effect 2, during loyalty mission, you have to choose between destroying  once and for all or commiting Heel Face Brainwashing on them.  leaves this decision to Shepard because he can't decide.
 * In the Homeworld backstory, the player race (Kushans AKA Hiigarans) were an aggressive, expansionistic race that the Taiidans battled and had nearly extinguished. The galactic outcry for mercy was such that they allowed the Kushan to leave and settle on a planet in the galactic rim after swearing to never use/develop FTL drives. Thousands of years later, the Kushan history is forgotten and their descendants discover the remnants of their original ship. To escape their dying planet, they set about repairing its FTL drive...
 * Also, the Taiidan are treated this way at the end of the first game, and are allowed to live mostly unmolested (save for having their very evil emperor killed).
 * In fact, the Hiigarans were so bad that the Bentusi had to interfere in order to stop them from wiping out the Taiidani. The reason the Taiidani kicked out the Hiigarans from the homeworld in the first place was because the Hiigarans have turned the Taiidan homeworld into an unlivable hellhole with orbital bombardment. Furthermore, had the Hiigarans peacefuly given up their hyperdrive core instead of attacking the Bentusi, they still would've had a fleet to defend against the vengeful Taiidani.
 * In the sequel to In Famous you spend the game getting enough power to use the RFI to stop The Beast, but it turns out
 * A major plot point in the Warcraft 'verse. After the end of the second war, the leaders of the Alliance were split on what to do with the (at the time Always Chaotic Evil) surviving Orcs. Stormwind and Lordaeron felt they should be spared, while Stromgarde and Gilneas wanted to execute them. Eventually, the decision to put the Orcs into labour camps in hopes that they could eventually be reeducated into proper members of society was made. This decision led to the latter two nations leaving the Alliance, though Gilneas would eventually rejoin during the fourth war.
 * Not just once. The orcs are tricked by Kil'jaeden into killing the majority of the Draenei. Several of them are clearly torn, as they know some of the Draenei personally and have a hard time believing them to be the monsters Kil'jaeden claims they are.
 * In Star Control 2 the Ur-Quan have one of these. After being enslaved for thousands of years by malevolent aliens and having to spend decades wired to artificial pain devices to defeat said aliens, they decide that the hat of Always Chaotic Evil fits all other species enough to warrant galactic conquest. They split over whether it's better to lock them up or kill them just to be sure.
 * They not only split, they actually start a millennia-long war over it. The victor will decide the eventual fate of the galaxy.

Web Originals

 * In the backstory of Mark Rosenfeldter's Constructed World of Almea, after the humans finally defeat The Empire of the Always Chaotic Evil ktuvoks, the kings of the two human countries who brought them down discuss among themselves whether or not they should just march into the swamps and kill every last ktuvok, so that they could never enslave and brainwash humans again. They ultimately decide against it, because "they did not have the stomach for it." Of course, this turns out to be a bad idea, because the ktuvoks rise again.

Webcomics

 * Order of the Stick. After a dragon threatens his family, Vaarsuvius kills the dragon, then briefly revives it so V can cast "Familicide", which kills the dragon's entire, very extended family. Since the entire dragon species only has about 4 family trees, and proliferate very slowly, this may well have doomed the species to extinction. V casting this spell is treated like a major case of Jumping Off the Slippery Slope, regardless of the fact that black dragons are Always Chaotic Evil.
 * Subverted by Eridan in Homestuck; he hates the terrestrial portion of the Alternian troll population, and claims that he would happily eradicate the lot of them, even commissioning a (land-dwelling) friend of his to build doomsday devices (that unaccountably fail to work). But by the start of the comic, the other trolls have figured that his aquatic-supremacist rantings are all just a cry for attention, and that if Eridan were given a genuine opportunity for genocide, he would pass it up.