Normally, when a villain who's a Bad Boss kills off a minion, it is for You Have Failed Me or You Have Outlived Your Usefulness reasons, but not always. Sometimes, the minion in question is too good at their job, and their superior will off them themselves (or congratulate the heroes if they do).
The reasons for doing this vary, but are generally some combination of fear of the minion becoming The Starscream, fear that a particularly unstable minion will ruin the boss' schemes, and Even Evil Has Standards.
The Dragon-in-Chief is often a target of this, although by their very nature they may survive such attempts to get rid of them by an inferior villain.
Very common in Real Life dictatorships since holding on to power in such an environment automatically breeds paranoia, leading to the ruler's inner circle gradually getting depleted until only the Yes-Men are left (unless one of the minions manages to bump the ruler off first).
- In the Mega Man X4 manga, Repliforce sub-commander Frost Walrus is a hotheaded Reploid with a penchant for causing destruction. In fact, his destructive nature got him marked for termination as a Maverick, but before he could be punished, the General did him a favor and saved him by inviting him to join Repliforce. Walrus engages in multiple riots during Repliforce's coup d'etat against the human government, many of which are not even helpful to the cause but are just destruction for destruction's sake. This eventually causes him to be rebuked by the Colonel, who says he will report Walrus to the General and tells him to stop causing wanton destruction. And what does he do next? He throws a temper tantrum, slams the ground, and decides to do the same thing he was warned to stop doing. He releases dozens of Reploid prisoners he has kept in the base and proceeds to slaughter them all one by one, with one Reploid being saved by the timely intervention of Hunters X and Blizzard Buffalo. Walrus's strength is too much for them, and he knocks X out while ruthlessly impaling Buffalo with a Frost Tower. When X comes to fight him again at his base, the Hunter destroys several of the ice cases of Reploid bodies in Walrus's base, infuriating him. Walrus is then heavily injured by X destroying the fuel tank of a Ride Armor, but he still recovers and gains the upper hand. General then brutally shoots him down and kills him to save X's life, and as punishment for his previous sociopathic behavior.
- In Dragon Ball Z, Freeza blew up an entire planet because he was afraid the Saiyans who served as his low-class soldiers could grow to overpower him. As it turns out, this was a legitimate concern, and despite (or perhaps because of) his extreme measures, it eventually happens.
- In Dragon Ball Z: Broly The Legendary Super Saiyan, King Vegeta commands his subjects to kill Broly who was just born that day because his battle power was too high for a Saiyan his age and might become a danger to his family. Broly survives the destruction of the planet Vegeta and becomes an Ax-Crazy Omnicidal Maniac.
- In Dragon Ball Super: Broly, King Vegeta sends the toddler Broly into exile because his power was too dangerous for the Saiyan race and tells the toddler's father Paragus that he should consider it lucky that he didn't order to execute Broly instead. Case in point, even as an adult, Broly has little to no control over his immense power and is a danger to anyone.
- In Baccano!, Mafia Don Bartolo Runorata sets Gustavo Bagetta up against the Gandor Family in order to get rid of him after Gustavo becomes more trouble than he's worth. In the anime, Don Bartolo ends up blowing Gustavo away personally as a gesture of good faith to Eve Genoard; in the Light Novels, Luck Gandor does the honors, but not before pointing out to Gustavo that Don Bartolo is aware of his shenanigans and will be glad to be rid of him.
- In Bleach, Kugo Ginjo advises his partner Shukuro Tsukishima to dispose of Moe Shishigawara after they're done with the Shinigami because his Fullbring ability could be too powerful for either of them. Even Tsukishima says this is a dick move. On top of that, Shishigawara is only Tsukishima's lackey, not a member of Xcution. It never happens, though. Due to both, Ginjou and Tsukishima dying, although Tsukishima finds comfort in his last moment with his loyal lackey Shishigawara.
- In the sequel to Tokyo Ghoul, it is revealed that CCG has policies and contingency plans for disposing of the members of the experimental Quinx Squad if need be. The members are aware of this and seem to accept it as a reality of their situation.
- Yang Wenli in Legend of Galactic Heroes is on the receiving end of a nonlethal version. After becoming a public hero to the Alliance, the politicians of the Alliance views him as an immense threat should he ever decide to run for office and they take every chance they get to smear his reputation, hound his operations through bureaucracy or congressional hearings, or outright playing the Uriah Gambit on him in the hopes he'll fail and his reputation will be ruined.
- One Punisher story has Frank go back in time to the Prohibition and get a job with Al Capone (by demolishing some of his goons in seconds). He brings his enthusiastic aid in taking out other criminal gangs, and soon Capone is holding a victory banquet... where the guests are tied up and he walks among them with a baseball bat, beating up traitors and those who've displeased him, explicitly invoking this trope when it's Frank's turn. Frank gets rid of the rope and kills Capone (no Capone, no Mafia; no Mafia, no shootout in Central Park where his family was having a picnic...). And then it turns out it was All Just a Dream.
- Dufayel, the Big Bad of Old West, eventually decides that keeping Henry around any second longer in not worth the risks and has Ramirez Arvenga to injure him and push him near the office's window, after which Dufayel shoots Henry, sending him falling down. Henry survives his fall though and flees the scene to have his vengeance another day.
- In The Three Musketeers, Richelieu is happy for this reason when the heroes kill Milady and gives D'Artagnan a promotion/job as a reward. While the Cardinal was willing to use her services, he's Affably Evil (and later books dropped the 'evil' part), whereas she was a psycho vamp and thus he was happy to be rid of her.
- In Hogfather, Lord Downey, the head of the Assassins' Guild, is shown considering the possibility of offing Psycho for Hire assassin student Jonathan Teatime. It's partly Even Evil Has Standards, but also practically speaking, Downey knows that Teatime is stealthy enough to sneak into his study undetected and crazy enough to kill him if the whim should take him.
- In Shards of Honor, Emperor Ezar turns out to have deliberately launched an invasion which was doomed to fail, so that he could kill his son Prince Serg and discredit the violent nationalists at his court. The sacrifice of numerous innocents during that invasion made it possible for the throne to pass to Ezar's grandson, Gregor, who is a noble and benevolent Guy Wearing the Kingly Mask. Ezar himself not only confesses to it all on his deathbed, but makes it clear he's looking forward to dying. And hoping there's no afterlife.
- In Joseph Conrad's novel Under Western Eyes, one character (based on a real person) is a Psycho for Hire who has infiltrated the Bomb-Throwing Anarchists. He's a Tsarist agent whose employers basically give him carte blanche to kill his own allies and basically conduct false flag operations to make anarchists look bad. After he severely injures the protagonist, a Hero Antagonist Secret Police officer lets the anarchists know of the traitor in their midst, and there's a description of the psycho being cornered by anarchists on a train with an implied Gory Discretion Shot.
- In the ninth and final (that was the plan, anyway) book of the Alex Rider series, Greater-Scope Villain Zeljan Kurst is well aware that Levi Kroll is angry over being repeatedly passed over for leading an operation, and arranges for him to be assassinated at the next meeting of Scorpia executives. This not only gets Levi out of the picture, but also allows him to use Levi's corpse for an Uriah Gambit that MI6 walks right into.
- Takashi Kurita attempted to eradicate Wolf's Dragoons (a powerful mercenary company who were under contract to him) because of his disdain for mercenaries and paranoid belief that the Dragoons would turn on him when their contract ran out. This despite the Dragoons' at this point very well-established rule of not accepting contracts to fight former employers.
- It was hinted (and eventually stated outright in Betrayal of Ideals) that the reasons for The Not-Named Clan's Annihilation was due to this. Nicholai Kerensky saw Clan Wolverine as too powerful and too independent, and unwilling to participate in the Proud Warrior Race society he envisioned if it would weaken their effectiveness, and manoeuvred them into direct conflict with every other Clan and had them all wiped out.
- Sigma in Mega Man Xtreme 2 thanks X and Zero for taking care of Berkana, saying she went too far and was too greedy with the power she was taking.
- Final Fantasy IV: After you defeat Dr. Lugae, you meet his superior, Rubicante. He then claims Lugae's actions were horrific, even for him and states he doesn't hold anything against you. A boss fight still ensues, but he is generous enough to heal the party first.
- Subverted by Emperor Gestahl in Final Fantasy VI: let's just say that trying to kill Kefka on a floating continent hundreds of miles above the surface is a BAD idea, especially when Kefka is wielding the power of three gods combined.
- The remake of 007 GoldenEye has the Big Bad of the first level shoot a minion who fired randomly into a room full of nuclear warheads. Taken right from the movie.
- After you kill Krauser in Resident Evil 4, Saddler contacts you and asks how he can thank you. Krauser was actually a double-agent working for Wesker and Saddler knew it.
- Knuckles from Ghost Master suffered this fate. One night at the casino, he caught the croupier cheating so that his Don would win every time. Since this moment could ruin both the croupier and Don's reputation, Knuckles was shot on the spot. They definitely shouldn't have done it: though his body was disposed, his ghost remains at the casino - vengeful and really powerful.
- In Faery: Legends of Avalon, it turns out that this is sort of what Oberon (the king) did to you before the start of the game, except he put you stasis rather than kill you outright. He tries to defend himself by pointing out that although he froze you, he's also the one who woke you up again (although that was just because he needed your services again).
- In Command & Conquer: Red Alert 2, Yuri assassinates Premier Romanov to seize power and then orders you to kill General Vladimir, who was already suspecting Yuri's motives and had been framed for the murder. The Player General continues to serve Yuri for a while until his continued success makes Yuri wary of a new threat. Lt. Sofia reveals Yuri's treachery before you can take him up on his invitation to visit him in Moscow, however, instead bringing half the army with you.
- Attempted in Mercenaries Playground of Destruction. Sergi, the leader of the local Russian Mafia branch, becomes increasingly paranoid of Josef, the Hypercompetent Sidekick who was sent to keep an eye on him and make sure that he didn't screw things up. This leads to Sergi selling both Josef and the player character out to the North Koreans, at which point Josef, who had until then been completely loyal due to being a strict follower of the Russian Mafia's code of conduct, turns around and takes over the operation, paying you to eliminate Sergi.
- At the end of Ghost of Tsushima, after Jin Sakai has given everything to save Japan from the Mongol invasion, the Kamakura Shogunate thanks him by declaring him a war criminal and ordering his immediate execution. Officially, they do so because of the dishonorable tactics Jin employed against the invaders. Unofficially, they're doing it because Jin's growth into a Living Legend and inspiration of the peasantry is endangering the feudal caste system that keeps them in power; it wouldn't do for the lowly commoners to forget their place and get ideas about standing up for themselves without relying on samurai masters for protection.
- In Tyranny, optional correspondence with Fatebinder Myotis reveals that Kyros regularly sends out Bleden Mark to 'cull' anyone who looks like they might develop Archon powers in their empire. Bleden Mark will attack the Player Character in three of the four endings of the game no matter your other actions up to that point, implying that you have just become a liability to Kyros. It's furthermore implied that Kyros' command in act III is a part of a mass culling of Archons present in the Tiers, since no matter the route you play at least two Archons will be dead by the end of it.
- In a print-only bonus strip of The Order of the Stick, Xykon and his minions retake his backup lair from the Good-aligned monsters that had taken up residence. The boss of the dungeon is a silver dragon (the same one that gets zombified later); one of the hobgoblin mooks lands the final blow. He gains so many levels that Xykon immediately kills him because he's too powerful to be a minion anymore (and because he's now a high enough level character that Xykon can actually get some experience for killing him).
- Non-lethally downplayed in True Villains, where Xaneth hits the Evil Sorcerer Bayn with a spell that de-powers him and de-ages him to an eight-year-old body the moment Bayn becomes powerful enough to worry him. As Xaneth explains, it doesn't do to be weaker than your minions. Bayn is grumpy about the situation, but continues to work for Xaneth in his reduced capacity.
- Our Little Adventure is set in an RPG-Mechanics Verse where the Big Bad Duumvirate prohibit any of their subjects from reaching Character Level 17, on pain of death. Zig-zagged when they nonchalantly kill Janice for that reason and trap her soul, only to bring her Back from the Dead at Level 16 because they don't want to waste a useful minion.
- The Evil Overlord List permits this, but only on the understanding that the Evil Overlord is then forbidden to ask why he is Surrounded by Idiots.
- In Worm, Coil decides to kill Skitter after she helped his plan to conquer Brockton Bay reach fruition, as he knows that she would oppose his continuing to hold Dinah Alcott prisoner.
- In Star Wars: The Clone Wars Darth Sidious ordered Dooku to kill Ventress. Sidious feared that Ventress had grown powerful enough that Dooku might turn her against him. This was a legitimate concern, as it's common practice for a Sith apprentice to seek out an apprentice of his own when betraying the Sith master...and Expanded Universe stories had depicted Ventress repeatedly advising Dooku to do exactly that (with herself as the new apprentice).
- Transformers: Prime
- The second season has Megatron deciding, after Airachnid tried to pull a mutiny and proving herself more competent than old Starscream, to cut his losses and order her execution. Airachnid manages to escape killing Breakdown along the way and decides to become a full-out rogue determined to finish off both Megatron and the Autobots.
- The third season initially centers on the Decepticons trying to revive the Predacons, a long-extinct type of Transformer. When their first successful clone, Predaking, turns out to not only be immensely strong but smart, independent, and ambitious, the Decepticons realize an army of Predacons would inevitably and successfully revolt—probably lead by Predaking himself. They decide to secretly destroy all the fossils planned to be cloned and frame the Autobots, getting rid of them while also distracting Predaking from any ideas of taking over.
- The Batman: The Animated Series episode The Man Who Killed Batman follows milquetoast feeble rookie goon Sid "The Squid" Debris as he's threatened by the entire Gotham underworld in one way or another for (accidentally) appearing to kill Batman. After a Whole Episode Flashback his boss, mafia kingpin Rupert Thorne, showcases he's yet another of the brutal and stupid men that Sid's run into all night long by believing that Sid is just applying Obfuscating Stupidity and trying to shoot him in order to prevent him from becoming a threat to Thorne's power. Thankfully Batman (who faked his death and had been following Sid all along to find out who was his boss) chooses to barge into Thorne's penthouse right then.
- Surena, the Parthian general who defeated Marcus Licinius Crassus at the Battle of Carrhae (very much a real-life Curb-Stomp Battle; Surena's 10,000 strong all-cavalry army defeated seven legions (about 50,000 men) while suffering less than 100 casualties), was executed by the Parthian emperor Orodestes II shortly after his victory because of this trope. To add insult to injury, Surena had been a core supporter of Orodestes in his just-finished Civil War against his brother Mithridates.
- Following his great success against Nazi Germany during World War II, Georgy Zhukov suffered a nonlethal example of this trope: Joseph Stalin saw him as a political threat due to his stellar reputation with the people and the army, and in 1946 had Zhukov demoted and Reassigned to Antarctica (as well as having him accused of looting and mismanagement, charges that didn't stick). Stalin actually wanted to have Zhukov killed, but the general was so popular at the time that not even Stalin could get away with this without risking dangerous instability in the military.