In Alan Moore's Miracleman, the titular character executes the innocent Johnny Bates to permanently prevent his evil alter-ego Kid Miracleman from resurfacing. Subverted in that Miracleman had already thrown a bus full of people at Bates/Miracleman without a second thought. The caption implies he did so while with at least partial awareness of the innocent deaths that would cause. It didn't hurt Bates anyway. Which Miracleman may have known.
Miracleman also kills Gargunza's dog to stop it from turning back into a monster. With a rock.
Ozymandias's plan in Watchmen is a nuke the dog. Then later he has to disintegrate his beloved pet, a genetically engineered lynx, in an attempt to destroy Dr. Manhattan
"I can't defend it. It was probably wrong... but... things aren't always black and white, are they? Sometimes I guess things get so gray you can't do what's right... only what's going to be least wrong."
Thorgal has one case of this when Thorgal and Shania end up petitioning one of the gods for the return of Thorgal's wife. Said god lives on a box floating in the middle of a void filled with threads, with each thread representing a single human life. All the god requires to return Thorgal's wife is for Thorgal to take his bow and fire an arrow in any given direction, which will be certain to at some point sever a thread and kill someone. When Thorgal can't bring himself to do it, Shania takes the bow from him and does it instead. The thread she severs turns out to be her own.
One absolutely heartbreaking example appears in Ultimate X-Men. An unfortunate teenager wakes up one morning and discovers that he's a mutant whose sole ability is to emit anInstant Death Radiusof a few hundred feet that kills every living thing around him. By the time he realizes what's happening, he has unwittingly killed his entire town including his family and friends. Frightened out of his mind, he hides in a nearby cave. Then Wolverine, who is able to survive thanks to his Healing Factor, appears. He gives the kid a beer and tells him what happened. In the end, to keep the kid from accidentally hurting anyone else and to keep his existence a secret (since news of a mutant with that kind of power would destroy any chance of peace between mutants and humans), Wolverine kills him. By that point it's almost a Mercy Killing since the kid can't live with being responsible for so much death.
In The Walking Dead, one of the children in the group, Ben, kills and cuts apart his twin sibling. This prompts an eight-year-old Carl Grimes, son of the protagonist, to shoot Ben, because he was "too dangerous".
In Green LanternCorps #66, the combined corruption of Parallax and the Black Lanterns have made it impossible to heal Mogo. As long as Mogo is active, he will continue to send out Parallax corrupted Green Lantern Rings across the universe, dooming countless billions to die by the hands of those who should be their champions. Faced with no alternative, John Stewart channels Black Lantern energy and ''destroys Mogo''.
John Stewart has become kind of a magnet for this sort of thing lately, as he also recently killed a fellow lantern who had broken under torture and was about to give up the access codes to Oa.
Also, Wonder Woman snapping Maxwell Lord's neck, in order to break his mind control over Superman. The latter wasn't too happy when he found out.
X-23 is forced to do this literally by the Facility as part of her Break the CutieTraining from Hell. When they decided she still had too much empathy for others, Laura was given a puppy with orders to kill it within a set amount of time and was then left alone to carry it out. She played with it instead, and when her handlers returned to find the puppy still alive threatened to torture it as punishment for Laura failing to follow orders, before relenting an offering her another chance.
In Uncanny X-Force, it is revealed that a resurrected Apocalypse will bring about the Age of Apocalypse. To prevent this, X-Force, an already morally ambigious team that's entire purpose is to Shoot the Dog, decides to kill Apocalypse. However, it's revealed that Apocalypse is actually a child, who is still innocent. The team is split, with Angel the most adamant about killing Kid Apocalypse, saying that Kid Apocalypse won't be able to control his nature, and that doing this will save millions of lives. However, he stops himself, and the team decide to take Kid Apocalypse back for training. Then Fantomex shoots him in the head. Later on, Deadpool of all people is the one to call the team out on this, and Wolverine says it was the right thing to do, and that sparing him was just a moment of weakness. Fantomex himself secretly cloned Kid Apocalypse.
In the Marvel UK event Revolutionary War, Mephisto has brainwashed the hero Killpower into leading a demonic invasion of Britain for him. In the final issue, his former partner Motormouth manages to re-access his heroic personality, who begs her to kill him before Mephisto reasserts his control. Motormouth refuses, as she's a hero, but Colonel Liger of the Warheads, Major Hauer of the Supersoldiers, and Death's Head I and II point out that they are most certainly not heroes and empty copious amounts of lead into him.
In one arc of The Authority, a woman comes to the team claiming to be three-year-old Jenny Quantum's mother. In fact, it turns out she's Jenny's twin sister, Jenny Fractal, with all the same reality-warping powers, but absolutely insane because she was kidnapped and brainwashed by a government conspiracy. Fractal kills Jenny and tears a hole in the fabric of reality that will destroy the world. The only way to stop her and save Jenny is for Midnighter to go back in time and murder Fractal as a helpless baby, just hoping he can tell the difference between her and his daughter. It works, but he was very reluctant to do it, and can barely stand to look at Jenny once it's over. He might be a textbook Sociopathic Hero, but that's a line even he feels rotten for crossing.
Night Of The Shy: After Fluttershy is possessed by the Big Bad, Nightmare, the rest of the Mane Cast reluctantly discuss the possibility that if all else fails, they may have to kill Fluttershy in order to defeat Nightmare. Princess Luna actually attempts to do so during the Battle of Ponyville but is Out-Gambitted before she can strike the killing blow and is killed herself.
In the Pony POV Series, this is how the Alicorns and Draconnequi justify destroying the G3 world and triggering a Cosmic Retcon. If they hadn't, the errors in that world would have caused it to collapse anyway and destroy everything. At least their way allows the world to start over again; they even state they wouldn't be doing so if they had any other choice.
Similarly, this is why, after the universe reboots, Destruction prevents the transition from G2 to G3 by basically nuking the planet at the critical moment. Sure, millions die and pony civilization collapses back into the Dark Ages, but if he hadn't, the Cosmic Retcon would have been rendered pointless.
Pandora, the Draconequus of Imagination, had no choice to imprison her child (the entity that would eventually become General-Admiral Makarov) in her box after it went on a rampage and turned the Realm of Legends into its own twisted fairy tale, despite clearly not wanting to. Later on, she has to help Shining feed Makarov to the Blank Wolf to save the entire world, and more or less sees doing so as this trope.
In Jewel Of Darkness, Falcon convinces the Endless Council to send an assassin after Midnight in order to prevent Trigon from using her as his portal. The justification he gives is that as she's evil, she's more easily corruptible than other versions of Raven, which means that there's a greater chance she won't defeat Trigon, allowing him to conquer that universe, and later the whole multiverse. He presents this as the Lesser of Two Evils.
Rise of the Galeforces: Violet feeds Ludlow to baby T.rexes. In front of everyone. Though to be fair, Adam did imply several times before that Ludlow thoroughly deserved it.
The Powers Of Harmony: When Cetus first reveals herself, Luna and Shining Armor try to kill her, despite the fact that she's possessing Rarity. Shining actually points out that everyone else will be upset with them, but Luna views it as a necessary evil.
In the Teen Care Bears series the Care Bear Magi state that thsi is their purpose: they were created to take ont eh burdens and perform the actions that the main Care Bear Family cannot, specifically to kill threats to peace and caring that cannot be reasoned with. Their first major series of actions is to systematically kill every member of the Hunters, and organization that pathologically fears and attempts to destroy all forms of magic, as leaving them alive might cause most of humanity to turn on the Care Bears; in a later story they seem determined to kill Fauna because she's been corrupted by No-Heart and might pose an unstoppable threat to everyone if she's left alive.
In the Tamers Forever Series, we have Takeru's plan to allow Takato to die in order to prevent Daemon from aquiring the power of God.
Fallen King has Joey throwing Ryou Bakura off the helicopter to his death.
"I'm protecting my friends," [Joey] replied. Though his voice was steady, his body trembled fiercely. Things had certainly changed. "He's not our friend."
In Order In Chaos, a Centauri patrol destroys an Orieni explorer, and interrogates the survivors to find out how many other ships were with them before they lost contact. The Orieni ships had been infected by an horror who feeds on people's mind and reproduce by infecting those who escape alive, and they couldn't allow any of them to reach an inhabitated planet.
Mirrors Image: Queen Chrysalis was forced to let her first daughter die of starvation, rather than let the entire Changeling Hive die trying to feed her.
In 2008, Batista confronted Shawn Michaels for doing this to Ric Flair and ending his career. Old Yeller was referenced leading up to the friendly match at WrestleMania 24, but - as was referenced in the color commentary for the match itself - it was rabies, not age, that forced the main character to kill the dog. Still, the match was presented as Shawn knowing full well that Flair was too old to wrestle any more and that he was going to lose to someone soon - all Michaels could do was fulfill his friend's wishes and be the one to end his career.
It's implied that Batista was jealous, because Flair asked Michaels and not him.
Shawn Michaels and Vince McMahon's actions in the Montreal Screwjob. Vince and Shawn really did screw Bret Hart out of the WWF Championship, out of Vince's fear that Bret would appear on rival promotion WCW with the title, since Hart was about to leave the WWF and go work for WCW. Something similar had happened before where then-WWF Women's Champion Alyndra Blaze dumped the Women's Championship belt into a garbage can on WCW's flagship program, Monday Nitro, and Vince didn't want the same thing to happen again. Hart refused to drop the title to Michaels, since the two had bad blood. Finally, at Survivor Series in 1997, as Michaels put Hart into Hart's own submission move, Vince called for the bell, costing Hart the match. Whether or not the real-life screwjob was justified or not is still a contentious issue among wrestling fans, even today.
the Imperium regularly Blows Up The Planet The Dog Was Living On in response to the worst outbreaks of heresy, daemon invasions, or alien threats. Billions are killed, but the alternative is generally much, much worse.
The number of times preventative measures such as Exterminatus are justified are balanced by the equal number of times in which they are not, but are used anyway because the people in power are deranged lunatics like the Monodominants. It is a rather grim setting after all.
All instances of Exterminatus are put under Inquisitorial review. If insufficient justification is found, the person who ordered it is sentenced to immediate execution, or to be killed on sight if they have already fled. Also, Exterminatus is not used nearly as often as certain parts of the fandom make it seem. Exterminatus being Flanderized into something the Imperium does if someone on a planet sneezes and it sounds vaguely like "Chaos!" is pure Fanon.
This is based on the real life way old fashioned armies operated. When a military unit (UK anyway) forms up to do drill, the NCOs are at the back of the formation and march behind the unit. They were originally there to shoot soldiers who ran from the enemy, as formation drill was originally about standing up with no cover in massed ranks and shooting at each other. The idea was that if you stand there and take the fire, there's a pretty good chance you'll be shot, but if you run the Sergeant will definitely get you.
In many countries desertion in the face of the enemy (as opposed to going AWOL) holds the death penalty if convicted by a Court Martial.
Including the US, though rarely invoked nowadays.
In Legend of the Five Rings, the Scorpion clan's 'hat' is that they exist solely to shoot the necessary dogs. The Scorpion, despite being traitorous bastards, are extremely loyal to the Emperor, and people who are worthy friends. Make sure you are one of those two, and preferably both.
A story explaining them: An author asks, in jest, each clan what the most important virtue is. Each clan picks one, and the Scorpions pick loyalty, while the Lions pick honor. The other clans laugh at the Scorpion talking of Loyalty, since they are traitorous bastards. The Scorpion proposes that each Daimyo will call his greatest warrior in, and give him a task. The one whose warrior does not hesitate, loses. The others are suspicious, but he talks them into it, offering to demonstrate the task first. He calls his warrior in, stares at the author, and gives her a look that says, "You know what I am about to do." He then says his command. "Kill me." Without hesitation, the Scorpion Warrior kills his Daimyo, then draws a knife and commits seppuku. Everyone else can only stare in awe.
This was pretty much Urza's whole hat in the original storyline for Magic: The Gathering. He had several thousand years to prevent a Phyrexian Invasion on his home plane of Dominaria. In the end, he started wars, killed thousands, ruined other planes (particular Rath and Mercadia), betrayed the person who was the closest thing he'd ever had to a son, sacrificed the lives of half a dozen other pre-sundering Planeswalkers, and was himself destroyed. When the smoke cleared, Dominaria was badly damaged, but still standing, while Phyrexia was a ruined husk, it's Machine-God destroyed in the process. Pity that It Got Better a few years down the line.
One bit of flavour in Eclipse Phase is a message from a Firewall veteran telling you how much of your career will consist of this and how shitty you will feel afterwards. One of the examples given involves a child infected with The Virus, and a handy airlock.
In Philoctetes, after spending ten years away from home caught in a war with heavy casualties, it's reasonable that if Odysseus knew of a way to end it soon and with Greek victory, he would pursue that course. That course requires bringing a crippled man he had personally wronged and left alone on a Deserted Island for years back to the war front. He is pragmatic in trying this first by deceit and then by force, because the man would never agree, but it's not very flattering for Odysseus.
In All My Sons, this is discussed when Chris is arguing with Ann about why he can't put his father in jail where he deserves to be. "We used to shoot a man who acted like a dog, but honor was real there, you were protecting something," Chris says. In this dog-eat-dog world, however, Chris doesn't see any sense in singling out his father for acting the way everyone else has to, even though "it just happened to kill a few people this time."
There was debate among the Schlock Mercenary fandom about whether Petey's making the Tricameral Assembly into an object lesson in the necessity of a healthy defense budget in the Teraport age by vaporizing them from orbit was a Shoot the Dog moment or falling through the Moral Event Horizon... However, the revelation that the "vaporizing" was just a show to scare the other governments into compliance, and that he'd merely teleported them away to draft them into his attempt to save the Andromeda Galaxy — and the universe in general — from hostile Dark Matter aliens made it pretty clear it's the former.
Baron Wulfenbach in Girl Genius apparently has to do this a lot. At one point the heroine has to be talked into leaving a situation for him to deal with because they know he'll do it. (The fact that as the ruler of most of Europe he's much better equipped to handle it probably factored in as well.)
In Dominic Deegan, Rilian the First Necromancer has taken the role of Dog Shooter several times, and is always ready to do so again. Rilian has killed Acibek on Acibek's request to seal the Storm of Souls the first time. He later killed the first Sylvan Oracle to deal with the Storm a second time. He's also let the Deegan's worst enemy threaten Dominic and his brothers as children, because he knew their mother would kill her to protect them. Later yet, he arranged for a "test" of Dominic and Luna, to see if Dominic was ready to Mindbreak; since Mindbreak is essentially a psychic Superpower Meltdown, it is a very bad thing. If Dominic failed any of the tests, Rilian was ready to kill him. Rilian noted once that his role requires him to be cold.
Immediately afterwards, it was revealed that Rilian was able to be his old jolly self around Dominic during the test, making the whole scene a rare case of Petting The Dog while holding a gun behind your back.
In a twist, while unaware of Rilian's plan, Dominic did check his future if he didn't go on the trip — definite Mindbreak and the mass murder of anyone within range — which, given Dominic is one of the more powerful psychics in his universe, is pretty darned big.
In Looking for Group, Cale'Anon on his quest to redeem his evil race through personal heroism, is railroaded by Forces Beyond His Control to murder a child in order to save the future. The child turned out to be the Arch-Mage in disguise (and he got better as soon as they left), so it was actually a Secret Test of Character.
In Harkovast, Quinn-Tain breaks Brightleaf's neck because he considers after she has already been disarmed and is helpless. He considers this to be essential to serve as a warning to others. This gets a furious reaction from Scatterpod. After she has gone, Quinn-Tain expresses regret, but still considers his actions necessary evils.
The Wild Zones of Zombie Ranch are populated with "practical sorts" who either lived through the Zombie Apocalypse or grew up knowing that zed bites are best dealt with quickly and with a minimum of fuss. The law's even on your side, as discussed here.
Towards the end of Act Five of Homestuck, Vriska is about to leave the trolls' hiding place to try to confront Jack Noir. However, Terezi, who has the power to predict the consequences of decisions, has foreseen that if Vriska leaves, Jack will follow her trail back and kill everyone remaining on the asteroid. Vriska refuses to listen, guessing that Terezi won't have the guts to stop her. She guessed wrong.
Later, Aranea drops a house on Jade, who really is part dog, due to said dog being under villainous mind-control that would only be continuously reapplied if she were to live.
Aram: See me shredding the papers? This is the only humane way to deal with them. Like putting a dog to sleep instead of letting it run around with a tumor in its brain. Beriah: ...Is that why Scruffy's gone? Aram: No, that dog was just ugly.
Survival of the Fittest character Adam Dodd was forced to euthanise his friend Marcus Roddy, as he had fallen into a coma. Most of the rest of his group didn't agree with the action, but Adam pointed out that had they left him catatonic, somebody else would have just come along and done the same, or he would have just been eaten by animals or some equally gruesome fate.
Among the many morally-grey choices characters make in Worm is, in Chapter 26.6, Weaver shooting Aster to prevent Jack's Slaughterhouse Nine from doing their thing and possibly causing the end of the world. What makes this example all the more depressing is it turned out to be meaningless as it was something else entirely that will cause the end of the world.
Happens a lot in Shadow Unit; one instance involved an actual dog, which (hidden for squick) a gamma nicknamed "Mrs. Chow" had started eating. Alive. From the middle.
Diddybob in Mind My Gap finds himself stuck on the mountains with his only son Jona screaming and crying his head off. Nothing he tries to sooth him helps and the cries become too much for him to bear. He's right at the end of his mind until he's interrupted by the man from the mountains. "You've got a gun in that frikkin suitcase no? What are you waiting for? Use it man!"
In The Penguins of Madagascar episode "Lost Treasure Of The Golden Squirrel", Skipper comments that money can't buy honour or respect - just as he looks into the Eyes of the Squirrel and sees himself buying an arsenal of high-grade military weapons to blow up hippies with as his greatest desire.
Happens several times in Justice League and Justice League Unlimited. These unpleasant-but-necessary duties seem to fall on Shayera "Hawkgirl" Hol's shoulders quite frequently:
In "The Savage Time", in the middle of a retreat, Green Lantern tells Hawkgirl to leave him behind so she can carry wounded soldiers out in his place. She does so without argument.
In "Starcrossed", she helps the Thanagarian invasion force defeat the League and conquer the Earth, because she believed the occupation of Earth was necessary to defeat the Gordanians, which was in the best interests of both her home planet Thanagar and Earth. (Though she draws the line at destroying Earth to save Thanagar, and she turns on her brethren upon discovering that they intend to do exactly that.)
In "Wake the Dead" Solomon Grundy gets reanimated through Chaos Magic as a raging, mindless zombie, and the only merciful option is to kill him (again):
Dr. Fate: (to Shayera) Your mace may be the only thing that can give the creature peace.
Green Lantern: What are you saying?
Shayera: Your favorite movie is Old Yeller, you know exactly what he's saying.
In "Epilogue", Shayera reached for the weapon designed to kill Ace, but Batman insisted on taking it himself to insure that things were done hisway.
The Question gets in on the act in "Question Authority". He struggles for months about how to prevent the events that led, in an Alternate Universe, to the Justice League becoming fascist rulers of the world—events that centered around Superman murdering Lex Luthor. Question's solution: go kill Lex himself (using his tie). After all, Supes is the ultimate good guy, and Question's a confirmed loony conspiracy nut. (Unfortunately, the real conspiracy Question uncovered in the process of confronting Lex was a bit more than he could handle.)
Word of God has it that only was Kyoshi actively advocating that Aang kill the Fire Lord. Yangchen's advice ("be prepared to sacrifice your spiritual needs") is ambiguous, as Yangchen was not necessarily stating that killing Ozai was the best option; she was only telling Aang that, if a better option didn't present itself, killing Ozai was a very viable option, and not something to be dismissed out of hand because Aang was feeling squeamish.
Sokka also has a tendency to this. At one point, he immediately leaps on a (somewhat poor) village's asking how they can be repaid despite Katara's Keep the Reward attitude, pointing out that trips across the world are expensive. He also goes back on a promise made to a powerful spirit who is disgusted by human belligerence (made on his behalf by Aang, no less) in order to discover information necessary for forming a strategy to defeat the Fire Nation. Notably, when Aang hesitates to "kill" a training dummy of the Fire Lord and asks how he can be expected to kill another human being, Sokka coldly lops the training dummy's head off with his sword and replies, "like that." Sokka acts as the team's Plucky Comic Relief so much that it's easy to forget that he's also the prince of a warrior tribe and has trained in warfare his entire life.
In Teen Titans, when Robin becomes Red X to uncover Slade's plans.
In the season 2 finale of Transformers Prime, Optimus Prime destroys the Omega Lock — thus ruining any chance of restoring Cybertron — in order to prevent Megatron from using it to terraform Earth and wiping out humanity in the process.
In A World Gone Mad, Jack Bauer-esque Anti-Hero Agent Griffin's whole philosophy is that someone like him has to do horrible things in order to protect the naive, peace-loving citizens who don't even know he exists. The joke is that he's horribly incompetent. So, not only does he kill civilians, cause the death of innocents, double-cross his own allies, and torture prisoners out of necessity, he often ends up killing, double-crossing, or torturing the wrong civilians, innocents, allies, or prisoners who have absolutely nothing to do with whatever evil plot he's trying to stop. It helps that he's a Sociopathic Hero and Karma Houdini.
A classic cover for the National Lampoon magazine features a gun being held to the head of a dog with the warning "If You Don't Buy This Magazine, We'll Kill This Dog". At the time the magazine was struggling, so the cover was intentionally controversial to inspire interest.
George Washington (hero number one in the U.S.A) has a Shoot the Dog episode among his many awesome moments. With the revolution in danger of falling apart due to the demoralizing effect of endless military defeats, Washington broke the traditional Christmas truce to lead troops across the Delaware River◊ and sneak attack a group of enemy mercenaries. The resulting lopsided victory had a crucial psychological effect.
The real reason for the disastrous Dieppe raid of 1942 was to ease considerable pressure on Britain to launch an invasion of France that year. Churchill chose to deliberately sacrifice 7,000 men, several Navy vessels and a lot of aircraft to make the point to Russia and America that any premature attempt to invade France would be a total and utter disaster and it was best to plan ahead and do it properly in 1944. He chose to have a battle Britain could not possibly win to make this point as dramatically as possible.
The atomic bombings of Hiroshima and Nagasaki remain controversial to this day, but those who defend them claim that, despite the horrific damage and cost of life, they prevented a longer and inevitably more bloody invasion of Japan. At the very least, they unambiguously saved the lives of almost every Allied POW being held by Japan. Their captors had orders to kill them if it was announced the Allies were actually invading Japan.
A more literal example caused the suppressed version of the Smith & Wesson Model 39 pistol to be called a "Hush Puppy." Its purpose was for special forces teams to covertly eliminate sentry dogs and guards without alerting the main target. There is also the more openly marketed "Velo-dog" revolver, specifically developed for early cyclists to defend themselves from dogs.
Another thing pretty close to literal is modern science's experiments on various animals, including dogs, for the sake of medical research. Whether you consider it justified or not, the reality is, many of the medical procedures that save lives today would not exist without experiments on animals, and if it weren't animals used as test subjects, it would be humans.
German soldiers in World War II actually had orders to shoot every stray dog they encountered on the eastern front on sight. This was the result of the Soviets experimenting with "anti-tank dogs" that had a bomb strapped to them, a triggering mechanism on their backs, and were meant to run under German tanks. The dogs were easily confused by the loud noises of the battlefields and had no way of knowing how to differentiate a German from a Soviet tank, and the project wasn't pursued much further. So the Germans decided to Shoot the Dog literally because the Soviets did figuratively.
Operation Catapult during WWII. Britain's main ally, France, has fallen to German forces and has signed an Armistice. Britain, resolved to fight on, is worried that Hitler will now be able to seize the well-equipped and trained French Navy. So the British launched a surprise attack on their former ally's fleet at Mers-el-Kébir. Caught completely by surprise by their erstwhile comrades, the French rapidly lost the battleship Bretagne and suffered crippling damage to the rest of their fleet. Britain would not be threatened by French ships, and would eventually be the jumping point for the liberation of France.