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. 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-Man is left.
- In Dragon Ball Z, Frieza 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 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 Shishigawa after they're done with the Soul Reapers because his Fullbring ability could be too powerful for either of them. Even Tsukishima says this is a dick move.
- 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.
- 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 MI-6 walks right into.
- 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 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, escpecially 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.
- 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.
- 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.
- 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).
- The third season of Transformers Prime 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.