In Tsubasa Reservoir Chronicle, at the end of the Koryo arc, Syaoran talks Chunyan out of killing the ryanban, but he is conveniently taken care of by his own previously mind-controlled servant.
One wonders what the The Omniscient Council of Vagueness group of old ladies who rule Japan (First Division) would have done to the cast of Mai Hime had Shizuru not gone crazy and killed them all after the cast kills their god. It's doubtful that they were resurrected along with the rest of the cast.
In Mai's fight with Shiho, she's unable to go on the offensive, realizing that as both of them consider Yuuichi their most important person, either of their Childs being destroyed will result in his death (Shiho, being overcome with jealous rage, fails to realize this). Yuuichi, not wanting them to fight, orders Mai to destroy Shiho's Child while fully knowing that he'll kick it, but she refuses. Then a brainwashed Mikoto jumps in, having been conditioned to attack Mai's enemy, and destroys Shiho's child. Yuuichi thanks Mikoto for this before he passes away.
In the 2003 anime version of Fullmetal Alchemist, the brothers need to create the Philosopher Stone. Problem: By episode 40, it became obvious that in order to do that, one needs to kill quite a lot of people. Solution: Scar did it. And died in the process.
Dragon Ball Z: Vegeta's entire purpose, story-wise, for being on Namek is to kill every single minor villain so the heroes (or at least Goku) don't have to. Cui, Dodoria, Zarbon, 4/5ths of the Ginyu Force (two while helpless!) and most of Freeza's mooks. Subverted in that Goku clearly doesn't want him doing this, and even calls him out after killing the two helpless Ginyu Force members. Also, Goku kills Freeza himself, or would have if King Cold didn't show up to revive him. But to be fair, Freeza DID kill a lot of people, including Krillin and (almost) Piccolo. Not to mention Goku gave him a Last-Second Chance twice; the second time when Freeza actually begged for mercy, before trying to kill him again.
Of course, the person who killed them has been frequently acting in their names, manipulating, or outright impersonating them for a long time now (all the decisions relating to Rukia's sentence were carried out by Aizen and his accomplices impersonating them), so it's hard to tell just how obstructive they really were...
Well, you have to keep up appearances unless you want people to notice that something is off, like the 46 members of the central government being DEAD.
And despite that, they've apparently assembled a new Central 46 within half a year.
Johan from Monster kicks off the plot by killing the corrupt doctors who screwed Tenma's career over. He also tends to kill any lesser villains who might be threatening Tenma or Nina.
In one episode of the Pokémon anime, the heroes arrive at a festival dedicated to the Pokemon Wobbuffet, and several party-crashers come and start destroying things. The festival people explain that since Wobbuffet can't hurt the enemy except by reflecting attacks, in honor of that they will not attack the party crashers. Ash & co know the guys must be stopped, but are unwilling to break the rules of the festival. Team Rocket, on the other hand, have no such qualms. Ass kickingensues.
This is so common in Magical Girl shows I'm not even going to list them but an example most western fans would be aware of is the big bads of Sailor Moon kill off most of their own subordinates who fail them which keep Sailor Moon and company from having to get their hands dirty. This is not the case of the Darker and Edgier manga however where they regularly kill their adversaries.
This courtesy does not, of course, extend to the Big Bad themselves or often to their Dragon. As more often than not Sailor Moon will kill them personally.
In Fairy Tail, after the eponymous guild is satisfied with just letting Grimoire Heart, the worst villains they faced so far who are clearly still evil, off with a scolding due to their leader being the guild's former master, Grimoire Heart leaves. As they lament their failure, Zeref, who they spent the entire series trying to get their hands on, approaches them. When they attempt to instigate their plan, he brushes them off, lets them know why he hates their guts, and makes their leader the third person in the series to be killed.
In Naruto, Sasuke played this role in killing Danzo, as there was no way for the good guys to get rid of him without a huge political mess because he was their acting leader at the time. His action enables Tsunade to resume leadership once she awakens from her coma without any complications such as a power struggle.
Shiva and Agora from Saint Seiya invoke the trope when they throw little Helen inside an active volcano. They even say that it's the best, since they had killed her grandfather and would've died anyway; in their words, after being offered as a 'sacrifice' of sorts, Helen's "pure and gentle" soul will become a benevolent spirit.Ikki obviously refuses to take this explanation and says they just went in full puppykicking mode. And uncommonly for this trope, Helen survives.
Discussed, but subverted in Rave Master. After defeating Hardner and learning about his sad past the heroes and their allies of the week are wondering what to do with him when Lucia comes out of nowhere and stabs him in the back, claiming they should be grateful that he solved the problem for them. Due to quick action, Hardner is instead saved and becomes the only Rave Master villain not to suffer from Redemption Equals Death.
This tends to apply frequently to the main characters of Apocalypse no Toride, although most of their actions could be written off as Villainous Rescue. One particular instance of this is Yoshioka stabbing another inmate through the hand and pinning him to a table to divert the zombies, giving them a chance to escape.
Doki Doki Precure has it in for Bel killing off Leva and Gula after they got defeated by Precure for the last time, effectively giving the team not only free from the duo but also getting their darkness to use it on Ira and Marmo.
Happens in Deadpool. A man who had been abusing Wade's friend is cornered by him, but unfortunately, she had earlier made him promise not to kill him. He leaves. Cue Taskmaster, who happily proclaims that HE didn't promise her squat. Cue Gory Discretion Shot.
James Robinson's Starman series had a great example. Starman and the golden age Green Lantern are confronting Mad Bomber Dr. Pip and his giant exploding suicide exoskeleton when their powers short out due to a Crisis Crossover that they aren't aware of. But◊ then◊ all◊ this◊ happens.◊
On the fourth page, note that The Shade is in fact flipping him off.
In Grant Morrison's Earth 2, the Justice League are in a universe where the bad guys always win, and are losing to that universe's Brainiac. Their solution is to walk away, allowing the evil Ultraman to lobotomize Brainiac with his heat vision.
The former page image comes from the SupermanY2K storyline. With Superman incapacitated and the city of Metropolis in chaos due to the apocalyptic Brainiac 13 computer virus, who is ruthless enough to step forth and protect the citizenry by any means necessary? Freakin' Lex Luthor, that's who.
Final Crisis also has Lex and Dr. Sivana coming to save the day from Libra when they hack into the Justifier helmets and kill Libra. Later, they helped the heroes build the Miracle Machine that fixes everything.
During Blackest Night, Hal Jordan allows himself to be possessed by Parallax again in order to fight the Black Lantern Spectre.
To give an idea of how desperate this plan was, keep in mind that the last time Parallax possessed Hal, he destroyed the entire universe. (But this is comics, so they fixed it.)
The remnants of The Black Glove that tried to utterly destroy Batman (and utterly failed) in Batman RIP could have caused problems in the future. It's probably for the best that Joker as Oberon Sexton killed them all.
Similarly, when Batman finally goes after the leadership of the Court of Owls, he finds that they've all already been killed by Lincoln March/Thomas Wayne Jr.
Averted in the American Sonic the Hedgehog comic. During the "Enerjak Reborn" arc, the Freedom Fighters are forced to fight Knuckles, who's been transformed into Enerjak and gone mad with power. Just when it starts to look like they might have to kill him, in comes Dr. Eggman, who captures Knuckles and intends to drain his life force to power his city. The aversion comes when Knuckles effortlessly breaks free and proceeds to level Eggman's whole city.
Played straight in a late comic where Shadow confronts Eggman, and outright states he's going to kill him. Eggman tries to play the Thou Shalt Not Kill rule. He turns out to be Wrong Genre Savvy, as Shadow points out; "Sonic holds such beliefs. But then, he's a hero... I'm not."
That technically counts as a Villainous Rescue since the Freedom Fighters and Dr. Eggman had invoked an Enemy Mine, and he did still save them. A straighter example occurs in the British Sonic the Comic, where during a break into Robotnik's city, during which his robot general Brutus turned him. Brutus, like in an earlier fight, was too powerful for the heroes, and who only get away due to him getting occupied by Robotnik fighting Brutus in a suit of Powered Armor, which ends with Robotnik freezing Brutus and smashing him into pieces.
In the Hulk tie-in to Fear Itself, M.O.D.O.K. and cybernetic villainess Zero/One teamed up to defend Manhattan from Skadi's forces
Wayne Shelton exploits this trope: the Big Bad is killed by another villain. Shelton confesses that he hoped him to do this. And call this a bargain with his own conscience.
In an early Thunderbolts story (#14), the Thunderbolts have to kill an alien leader in order to get out of the dimension they're stuck in. Even though he understands the necessity of it, Abe (MACH-I) can't bring himself to, and Moonstone has to instead.
In the X-Men graphic novel God Loves Man Kills, the X-Men and their erstwhile ally Magneto have captured a few of the enemy "Purifiers." The heroes are desperate for information about the Big Bad's plans, but the Purifier they question refuses to talk. Magneto, who at this point has yet to enter the Heel-Face Revolving Door, does...something...to the man to force him to answer.
Something comparable happens in Uncanny X-Men #269. Here Rogue and the personality she absorbed from Ms. Marvel come out of the Siege Perilous as two separate persons; unfortunately there is only life force for one of them to survive, and therefore the Ms. Marvel revenant (a separate being from Carol Danvers, who was then in outer space as Binary) tries to kill Rogue. Rogue manages to defeat her, but can't bring herself to kill her even to survive, and so "Ms. Marvel" turns the tables again. She is about to kill Rogue when Magneto intervenes and kills the Ms. Marvel revenant. This could possibly be interpreted as Magneto being a Combat Pragmatist, but the subsequent story (#274-275) shows him starting on the road to becoming a villain again.
Wolverine considers himself damned already because of his past, so he's willing to cross lines actual heroes shouldn't. He does not want anyone else, especially kids, following his example.
Transformers Autocracy: Megatron fights Zeta Prime, Optimus's Tyrannical predecessor, with Optimus himself (then called Orion). The battle is furious, and ends with Megatron shoving his Fusion Cannon up under Zeta's chin and blowing off a third of his head.
In Friends to the End, Hago kills Scar whilst his back is turned.
In The Interceptor's Challenge, the Interceptor rips Shocker's head off, before burying him underneath the ground for all eternity.
Queen of All Oni: So far, all of the villains killed off have met their ends at the hands of Jade or her minions.
Films — Animated
Simba from The Lion King is too moral to give Scar the killing blow. However, the hyenas who Scar tried to blame for everything when things started looking bad... they have no such morals. And they haven't eaten in a while...
The climax scene of Let the Right One In goes...this way, kind of. As the kid's about to be drowned, the Eli shows up and saves the day. But since she's a vampire, she kills three people doing so.
In Red Sun, the villains are about to kill the heroes, only to be interrupted by an attack by murderous Comanches.
The Joker did this in his own twisted way in The Dark Knight, when a Wayne Enterprises accountant discovered Bruce's big secret and was about to reveal it to the world on live television. But leave it to the Joker to take something that would have been a favor to Batman, and to twist it to his own ends:
Later on, the Joker strands two ferries in the middle of a river, one filled with civilians and the other with convicts, with each one (supposedly) having the detonator to the other ferry and ordered to either blow up one by a certain time or the Joker will blow up both. While the civilian passengers are heavily considering blowing up the convicts, in the convict boat, the warden (who is holding the detonator) is approached by a Scary Black Man convict...
Ginty: You don't want to die, but you don't know how to take a life. Give it to me; these men would kill you, and take it anyway. Give it to me. You can tell 'em I took it by force. Give it to me, and I'll do what you shoulda did ten minutes ago.The warden gives him the remote... and the convict throws itout the window]
In addition, Gotham City's top crime lords and their "accountant" are killed off by either Joker or Two-Face.
Straight example in The Dark Knight Rises: Batman's one rule keeps him from killing Bane. But Catwoman has no such restriction.
In the first X-Men film, the Mutant Registration Act is defeated due to the Brotherhood unintentionally killing the Act's main supporter and Mystique replacing him later on.
Chris Pine's character in Carriers where everyone is a Crazy Survivalistshoots the dog many times in order to spare his more innocent brother from doing it himself. It rubs off on his brother though, who later finally gets his hands dirty by killing Pine when he is infected.
In Bad Lieutenant Port Of Call New Orleans, the title character is being pursued by gangsters who want him to pay $50,000 for roughing up the son of a local real estate mogul. Rather than paying, he lures them to a place where he's meeting a drug kingpin that he's in business with. When the gangsters try to steal the kingpin's product in payment for what the protagonist owes, the kingpin and his men kill them all.
Elysium: This is what Delacourt keeps Kruger around for, to the dismay of President Patel. Then, when he gets to the Elysium near the end, Kruger kills Delacourt.
The Culture novel Matter has a Sealed Evil in a Can being released and in typical Banks fashion killing most of the main cast. While this is nearly all of the heroes, it also includes the Evil Chancellor who had usurped a throne and his minions. Thus, the Culture are able to set-up the surviving hero as the future prime minister, and unlike in other novels in the series, didn't actually have to act morally ambiguously and get rid of corrupt leaders themselves.
In Night Watch, Vimes frees prisoners from the Cable Street watch house. In the process, he has to subdue a torturer, who he leaves tied to a chair and forgets about until someone reminds him. Since he gets reminded after he started burning the place down, he has to run back in, all the while trying to decide whether to kill the mook, cut him free, or cut just enough rope that he can maybe escape before he burns to death. Luckily, Captain Swing shows up and kills the mook before Vimes has to make his choice.
Vetinari: In his own words “history needs its butchers as well as its shepherds” or, in plainer language “Magnificent Bastards do the dirty work.” note Swing also used the phrase.
“Stoneface” Vimes used more or less the same phrase, and executes the last king of Ankh in person, without any form of trial. To be fair, the king deserved it, and some of the comments about the event indicate that he tried for a trial, but there wasn't anyone willing to be judge.
In Bernard Cornwell's book Agincourt, the main character, Nick Hook, has made a vow to a priest not to kill the murderous rapists who his family has been in a blood feud with for generations. His arch-enemy, father-in-law, and prisoner (it's complicated) made no such promise.
In Harry Potter and the Deathly Hallows, the Pensieve reveals to Harry that Snape felt he was subjected to this when he was told to kill Dumbledore so that Draco wouldn't have to cross the point of no return.
To be fair to Aly, she was trying to find a way out of killing the children, and considered binding them magically to oaths that they will not try to take the throne and exiling them together with the royal bodyguard as caretaker. Unfortunately, she mentioned to the trickster god that the children were in her way. The god got impatient with pacifist methods and persuaded the regents that they would be better off without the boys.
In A Song of Ice and Fire, this is how Tywin Lannister endeared himself to Robert Baratheon who had just secured the throne. Robert knew the old Targaryen line had to be extinguished for his throne to stay safe, but "he saw himself as a hero, and heroes do not kill children." Fortunately for Robert, Tywin (or rather his men) had no such delusions and happily murdered the two surviving Targaryen kids in the palace (committing a few other atrocities along the way).
To a degree Tywin's son Jaime also gets this treatment, since he killed Aerys, the Targaryen king, for Robert and company. In Jaime's case though any relief and/or gratitude is tempered by the perception that he has Chronic Backstabbing Disorder, since he was part of an elite group of bodyguards who are supposed to be willing to die in order to protect the Royal House.
In the Dale Brown novel Executive Intent, the Chinese assault on and takeover of Mogadishu is likened to this In-Universe by one character, noting how China had solved the problem (Somali pirates, to be exact) most of the world probably secretly wanted to deal with but could not bring themselves to handle.
A weird meta example occurs in the first Warrior CatsMyth Arc. Firestar had to defeat Tigerstar, but being the classical Heroic Archetype he needed to beat Tigerstar with moral superiority. Unfortunately, Tigerstar's plan was actually beneficial to the forest, with it's only problem being that someone crazy and evil was designing it. The problem was resolved in the last book of the arc The Darkest Hour, when Tigerstar's ally Scourge betrays him and becomes the Big Bad, allowing Firestar to have an opponent he could kill by having greater morals.
The Hunger Games are about a competitiion where 24 children have to kill each other until only one is left standing. Luckily for the main character, a group of kids who went into the game by choice rather than by force are painted in a very negative light, and commit almost all of the unprovoked killings.
The Deverry Cycle has little Olaen. When the Deverrian civil war ends, five-year-old Olaen 'rules' the losing side. The choices to prevent future challenge are death, castration, or blinding, the later two involving turning him over to the priesthood to raise. Oggyn poisons the boy with 'Dwarven Salts'.note Wordof God is the salts are arsenic.
Ruahkini in The Quest of the Unaligned is an incredibly rude and borderline crazy Rich Bitch who is perpetually insulting Laeshana and patronizing Alaric, as well as being partially responsible for the destructive imbalance in Caederan's magic. Unfortuantely, he's also the royal chancellor, so there's no conceivable way for the heroes to get rid of him. Luckily, his Ax-Crazyhoshek brother Gaithim shows up and kills him.
"Wild at Heart": We don't kill werewolves, because they're human most of the time, but Oz's wolf side is amoral and thus free to kill Veruca.
Buffy can't kill the Anointed One, partly because she's prophecied not to but mostly because he's a kid. Luckily, Spike does it for her.
Buffy is dying after being shot by Big Bad wannabe Warren. Willow appears, heals her, and takes the bullet, which she uses to torture Warren with and become the new BigBad.
Buffy can't kill Glory without killing her innocent host Ben. Giles, however, is willing to so that she doesn't have to.
Dexter, end of season two. Sgt Doakes can prove that Dexter is the Bay Harbor Butcher, so Dexter locks him up in a lonely cabin until he can decide what to do. Dexter won't kill Doakes because he's a good guy. Lila, who is as psychopathic as Dexter but with no such code, finds the cabin and blows it up.
In a way, this trope is the entire premise of Dexter... Dexter is the Big Damn Villain, played straight whenever he interrupts a murder to abduct his target.
Farscape: In the episode "Prayer", it's ambiguous whether or not John knew Scorpius was going to kill the merged Chiana-Aeryn when he brought him along to the alternate universe, but it's what had to be done. See page quote.
In an earlier episode, Moya is in orbit around a planet with notoriously sexist laws, and accepts a visit from a mechanic- accompanied by an armed security guard. Things go well, up until Chiana discovers that the mechanic is actually a woman, rebelling against the government by doing a Sweet Polly Oliver; just when it looks like they're becoming friends, the security guard shows up and, infuriated that he's had a woman under his nose all this time, holds both of them at gunpoint. Given that there's almost nobody else aboard the ship at the time, it looks as though the two of them are going to die...right up until Scorpius calmly drifts past and snap the man's neck. All the more impactful because Scorpius had been having a friendly chat with the guard before then.
This has happened tons of times in Smallville. Clark has to face people with dangerous superpowers, and while he can beat them readily enough, he can't very well run a super-jail or convince them to lead an honest life because, well, Kryptonite gives most people a god complex, and most krypto-freaks aren't stable/good to begin with. Having Clark kill or permanently disable them is far too squicky for a proto-Superman to do, so the preferred solution is to have them depowered or hoist by their own petard. The other solutions that pertain to this trope are to have them be killed by evil infighting among themselves, or having Lionel (and later Lex) deal with them.
A big one in season nine. Both the Justice League and Zod have a bone to pick with Checkmate. Oliver and John get captured at different points, although they managed to escape. Chloe is also kidnapped and almost killed in an attempt to blackmail Clark into revealing more about their team. Zod, on the other hand? He comes over to visit and burns down their entire castle base with heat vision. Zod will not toleratehuman nonsense. Kneel Before Zod.
This is Michael Weston's modus operandi in Burn Notice. Michael is a Technical Pacifist and abides by Thou Shalt Not Kill, (except when he doesn't). This never seems to keep the Monster of the Week from dying in incredibly horrible ways at the hands of their boss or criminal rivals. In one of the more extreme examples Sam goaded three mooks into a Mexican standoff inside a house, and fired his gun into the air outside so that the three mooks would all pull the trigger at once and blow each other's brains out. Yipes.
Note that none of the main characters ever expresses a moral objection to killing. Most of the early episodes have an obligatory scene where Fiona offers to murder the bad guys and Michael explains why that would cause more problems than it solves. They're all okay with bad guys being killed, it's just easier to accept them as the heroes if they don't to it themselves.
In the third season of Heroes, a recently depowered Peter heads off with the Haitian to kill his father and destroy the Formula. However, once they get there they encounter problems when Peter can't pull the trigger as Arthur makes his saving throw to turn Peter to his side. The obvious solution? Sylar shows up, complete with recently stolen lie detection power, to ask Arthur if he's really a Petrelli. Naturally, Arthur lies, thus causing Sylar to allow the bullet he had grabbed in thin air to kill Arthur stone dead permanently.
Not the straightest example. While Sylar was the one who pushed the bullet into Arthur's skull, he was the one who stopped it in the first place. Had Sylar not been there, Peter would've been the one to kill Arthur, he just waited a while before he did it.
Sylar actually lampshades the fact that he prevents Peter from becoming a murderer. So actually he wasn't here to do the job, just to keep Peter from having remorses.
Battlestar Galactica: it's obvious midway through "Pegasus" that Admiral Cain is a dangerous psychopath who needs to be dealt with. Adama is too moral to go through with an assassination. Fortunately, Baltar has let a Cylon with a grudge against Cain loose.
Ironically just after Cain proved that she wasn't completely insane yet, having in turn just refused to assassinate Adama.
In one episode, Roslyn has Baltar in the brig and threatens to throw him out an airlock if he won't tell her what she wants. Baltar says that she wouldn't go through with it, so she brings in Col. Tigh. Even that was a bluff, but Tigh would have done it.
Da Ren Wu is a Chinese TV series based on a classic kung-fu novel set in medieval China. The heroes, as usual in wuxia literature, are staunch Confucianists: morally opposed to unwarranted violence and who don't approve of killing under any circumstances. At one point, Sisi, the main heroine, is tricked by some crooks who steal everything she owns and give her to a Masqueraded School for whores. The boss and his cronies take great pleasure in tormenting defenseless girls, and kill those who don't respond well to the training. Three characters come to Sisi's rescue, one after another: 1) Yang Fan is the first. He can't find Sisi in the School (the boss locked her in a hidden room), so he leaves convinced he made a mistake. 2) Qin Ge, a famous kung-fu master, is the second. He can't find Sisi either. He suspects something, but can't prove anything. He leaves as well. 3) The hunchback is the third. He's a major bad guy. He needs Sisi for some nefarious plan. He waits till night, gets into the School, finds Sisi and takes her with him. He pummels the cronies, and when the crossdressing boss tries to stop him: the hunchback pulls a Fist of the North Star on him. After leaving the School with Sisi, the hunchback tracks the crooks who had tricked her. He finds them, makes them give back the stolen stuff and beg for mercy on their knees...and then kills them nevertheless, just because! They say the author was very surprised when the hunchback's popularity with the audience skyrocketed after this story arc.
In an episode of Taxi, Elaine visits a trendy hair stylist(played by Ted Danson) and comes away with an atrocious hairdo. She, Alex and Louie pay the stylist a visit to demand an apology and he rebuffs them. Elaine considers dumping a bowlful of hair dye on the stylist's head but decides not to, declaring "I'm better than you." Before they leave, Louie(in a combination Crowning Moment of Awesome/Funny) casually dumps the hair dye over the stylist and says, "She might be better than you, (beat)...but I ain't!"
In the Doctor Who special The Five Doctors, the Master has been captured by the Cybermen and is initially being forced to do their bidding. He ends up turning the tables and wiping the whole lot of them out by skipping through a trap he's figured out the solution to, but conveniently forgets to tell his captors about.
Twenty-six years later, in "The End of Time," this same Master (well, different actor/regeneration) forces Rassilon back behind the time lock on the Time War, and won't let him take the Doctor with him, either.
Subverted in "The Pandorica Opens." a good number of the Doctor's foes all band together to save the universe...from the Doctor, who they've been tricked into believing will destroy it, when in fact he's the only one who can stop the explosion that will destroy the universe.
Torchwood: The trope gets played with. Captain Jack Harkness fills the role of the trope, despite not actually being villainous. Torture, murder, kidnapping, or any other action that would normally fall under this trope and require a villain to perform it gets performed by Captain Jack at the protest of the other characters.
This is one of the main ideas of Leverage. Sometimes bad guys make the best good guys.
When Nate goes for revenge on the two men behind his father's murder, Elliot warns him that straight up murder carries a much higher moral cost than their usual method of destroying a bad guy's life. In the end, Nate plays the two against each other (getting each of them to point out why they should want the other dead) then leaves them to fight over a gun with a single bullet. They both fall off the nearby cliff while fighting over the weapon.
Many episodes of Mission: Impossible involved manipulating characters associated with the target into killing them.
In "Good Form" of Once Upon a Time, Regina mentions that she could tear out the lost boy's heart and use that to control him to deliver the message to Henry. Snow White freaks out, but Emma tells her to do it. Later she says something to this effect when Snow White says she doesn't want Emma to have to do those things.
In Chris Carter's short-lived Harsh Realm the Three Percenters are a population of virtual zombies caused by a glitch in the program. They can convert just about anyone playing the game, and nearly do so to Hobbes and Pinocchio. Mel Waters sees through them immediately and he's the one who eliminates the threat.
In Advance Wars Dual Strike, the Big Bad is defeated and at the player's mercy. But the machine he hooked himself up to is still draining the planet, and he needs to be killed. Von Bolt taunts Jake, asking if he can really shoot a defenseless old man. The player is offered a choice of whether to shoot him or not, and if you don't, Hawke shows up and does it for you. The odd thing about this is that either way, the shooter just destroys Von Bolt's machine itself.
Reaver's job in Fable III is to do this. He stands in court to argue in favor of the evil option when making decisions as king. While these options are generally quite despicable and having an orphanage would be a fine and dandy in the long run, you could really do with the 1.25 million you'd make from opening a brothel right now to fight back the Eldritch Abomination that threatens to destroy Albion.
He also does this in the previous game. If the player does not kill Lucien in the middle of his Motive Rant, Reaver will take the chance to shoot him.
In Iji, if you're taking the pacifist path, two of the bosses get backstabbed by their underlings; conveniently meaning you don't have to kill them. This was actually added in, since earlier versions meant a completely innocent run was impossible.
In Fate/stay night, Ilya kills Shinji in Fate, saving Shirou from having to do it; Sakura does the same in Heaven's Feel. Sakura and Kotomine combined also kill off Zouken in the same route, who would probably have caused some moral quandaries since he's essentially defenseless on his own at that point even though his very existence is an abomination.
In Metroid Prime 3: Corruption, Dark Samus kills the corrupted Hunters after you defeat them. Samus probably couldn't bring herself to Shoot the Dog, making Dark Samus quite convenient in a twisted, twisted way.
A borderline example between this and Villainous Rescue occurs in Super Robot Wars 3. Anavel Gato's claim to fame in his show of origin is launching a stolen nuke at a peace conference. He reenacts this scene in the game, but this time the "peace conference" is between two villainous factions. What makes this a borderline example is the fact that the heroes congratulate him on this and gladly accept his Heel-Face Turn application, suggesting that they may have done the same thing if they had a nuke lying around.
In Drakengard 2, it transpires that one of the pact knights that keeps the Goddess Seal intact is Ulrich, a party member and Nowe's Big Brother Mentor, and must be killed to break the seal. Despite wanting to destroy the seal, Nowe can't bring himself to do it. Fortunately, Caim happens to be in the area and is more than happy to oblige, even it means having to go through Nowe to do it. Especially if he has to go through Nowe to do it, really...
Maximillian's on the ropes and the land battleship is about to explode; it's too dangerous to approach and Welkin and Alicia can't capture him alive! How do we solve this? Have Faldio show up out of nowhere, grab Max, and pitch himself into the exploding inner workings of the machine, killing them both. Again, the villains get their punishment, and our heroes are utterly unconcerned.
In Uncharted 2: Among Thieves, after defeating the Final Boss Lazarevic in a blatant example of Get It Over With, Lazarevic dares the protagonist to shoot him and end it. True to character, Nathan is not the one that has to end it. The Guardians, originally mini-bosses, arrive to finish the job for you.
In Assassin's Creed: Revelations, Ezio promises Suleiman that he will spare the Templar Leader, Suleiman's uncle, Ahmet if he can. During the confrontation, Selim, Suleiman's father and Ahmet's brother, interrupts, strangles Ahmet, and throws him to a Disney Villain Death.
Vriska from Homestuck attempts to take the fight to the Big Bad, and even The Omniscient thinks she might win. The price would have been leading the bad guy directly back to the Last Bastion and wiping out her race.
In The Order of the Stick, it falls down to Tarquin to kill Nale. Being Genre Savvy he also points out that with this he freed the plot from yet another recurring villain, wanting himself to be the important villain.
Incidentally, Nale's death was done partly because he killed Malack, Tarquin's best friend and the one who turned Durkon into a Vampire. This act also got rid of a potential threat in the form of a vampire, and freed Durkon his Thrall state, allowing him to rejoin the Order of the Stick.
When the Azn Bad Boys begin a bombing spree in Worm, supervillains of the town team up to attack the ABB's bases in order to remove that chaotic element from the table — and end up doing a lot more visible damage to the organization than the local superhero teams.
It's growing into a major theme, stretching from taking down the ABB, to going toe-to-toe with several major threats, to Skitter keeping the peace in her territory safer than it had been for years. People noticed, too. They noticed enough to shield her from an arresting band of "heroes".
In To Boldly Flee the crew of the USS Exit Strategy needs a bit more time to counterattack the villains, who are already locked on to them and might just win. Cue Mechakara, whom those same villains betrayed at the end of last episode, beating up the whole evil bridge.
Doomsday's first appearance in Justice League Unlimited. In the comics, he killed Supes (He got better). However, Supes' evil universe counterpart, Justice Lord Superman, used his eye lasers to lobotomize Doomsday not five minutes into the fight (he got better too, and was mighty pissed, but that's another story).
In Aladdin: The Series, in the episode "The Citadel", Aladdin threatens to turn a magic-eating monster loose on Mozenrath, who taunts him by pointing out that he's not ruthless enough to do that. "You're right. I'm not." Then Aladdin points at Iago, who is already poised to remove Mozenrath's control collar from the beast. "But he is!" And Iago proves it.
In Kong: The Animated Series, Ramone De La Porta is the main villain and constantly causes trouble for Jason, Kong, and the gang when he is trying to unlock powers of the Primal Stones, while often making threats and trying to kill Kong, yet they often save him whenever he is in danger (and he only returns the favor once, just so they're even). In the final episode, Harpy sucks De La Porta's life force out as part of a ritual to awaken Chiros. De La Porta survives when his life force is returned to him later, but is left in a permanent state of shock.
South Park is saved from hostile takeover by the Jersey Shore by Al-Qaeda.
In Insheeption, Freddy Krueger kills Woodsy Owl after the latter goes One-Winged Angel.
In The Movie, it's Satan who finishes Saddam off after he gets zapped by ten thousand volts of profanity courtesy of Cartman.
In The Batman, Wrath and Scorn have figured out Batman and Robin's identity. Even though they are arrested, Batman really can't do anything to keep them from revealing this to everyone. Luckily, the Joker (much like in The Dark Knight) didn't want someone else causing the end of Batman and gassed them while they were in the police van.
Tom Slick once raced against a cheater who, after being defeated, was told by Marigold he'd get his commeupance. He said good guys like Tom Slick don't get even. Then he got his commeupance from another racer wronged by his cheating.
In Powerpuff Girls episode Telephonies, the Gangrene Gang trick the Mayor into leaving his office, so they can use his hotline to send the Girls to pound on various other villains (who were actually just minding their own, non-villainous business for once). Eventually, said villains figure out exactly what's going on and proceed to open a can of whoop-ass on the GG.
So once again the day is saved thanks to Mojo ...Fuzzy ...and Him?!