This was revealed to be the case with GLaDOS from the Portal-series. Portal 2 reveals that GLaDOS used to be a woman named Caroline, who was forced into a Brain Upload against her will. This pissed her off so much, she'd try to kill the scientists within a sixteenth of a picosecond after being turned on. The engineers retaliated by hanging Personality Cores on her, effectively giving her artificial schizophrenia. In the tie-in comic Lab Rat, it's revealed that GLaDOS tricked one of the scientists into giving her control of the supply of neurotoxin. As soon as she had that, she locked down the facility and pumped the neurotoxin into the ventilation system, killing everyone inside (with the exception of Doug Rattman).
Knights of the Old Republic: Near the end of the game, after crossing the point of no return, you can decide once and for all if you are good or evil. Pick evil, and your fourteen-year-old Playful Hacker ally Mission will try to fight you. Her Wookiee pal Zaalbar will normally side with her, but you can call on the life debt he owes to youand force him to kill her. If you bring him along when you storm the Star Forge, he will turn on you, but by that point you're probably powerful enough to dispatch him easily.
Lisa Garland in Silent Hill. In the Good endings, she kills Kaufmann, who turned her into a drug addict and (possibly) killed her before, either directly or as a result of her addiction. It's likely that she took more offense on the latter one. Though the Lisa in the game isn't the real Lisa, just a construct controlled by Alessa, and Kaufman helped the cult do far, far worse things to her.
Subverted in Jagged Alliance 2. You'd think Eliot, the poor bastard that's been beaten up by the Queen the entire game, would be more sympathetic to the mercenaries that are about to kill the sadistic bitch. Not so much. In fact, if you take too long to get to the palace, you can't even bypass him: you have to kill him.
Played straight with the Warden's husband though; although thinking about it, his dialogue suggests he's pissed off from having to look after the kids all day while his spouse works and so he'll happily help the heavily-armed sociopaths, who just broke into his house, kill the sole bread-winner.
In Clive Barker's Jericho, the Firstborn is attacked and killed (presumably, it is never made clear) by Arnold Leach after the latter realizes that he was nothing more than the Firstborn's pawn.
There's a difficult-to-properly-understand scene in the end of Twilight Princess that implies that Ganondorf was betrayed by the new villain, Zant, who he had been using as a conduit. As Ganondorf struggles to maintain his willpower, and reaches deep within himself for new strength, we see a shot of Zant. Zant snaps his head to the side, as if cracking his neck, and Ganondorf dies. Maybe for the last time.
Except that by all appearances Ganondorf didn't abuse Zant, and kept both the letter and spirit of his promise, as Zant was indeed made the Twilight King (and worshiped Ganon as a god). A better example might be Midna going medieval on Zant after his defeat; this might also explain the above scheme seeing how Ganon's power was the only thing keeping Zant alive at that point.
They were brainwashed, actually. Darion Morgraine, commander of the Ebon forces, snapped out of it when the ghost of his father rose from the chapel they had just failed at assaulting. While it's not shown in the game, the Death Knight graphic novel implies that all of the Ebon Knights (or at least the ones that didn't return to the Scourge) had a similiar encounter with their own dead parents. So a better question would actually be: Was it really a good idea to play the We Have Reserves game on your elite forces on the holy ground where their ancestors rest?
In the Halfus Wyrmbreaker encounter, players must free the enslaved drakes around the arena, who put a debuff on Halfus that prevents him from using his abilities as effectively (for example, one reduces the amount of damage Halfus' proto-drake does, while another enables tanks to get an occasional reprieve to clear their debuff stacks). They are mind controlled and must be killed afterward, but killing them puts a damage-increasing debuff on Halfus.
Do NOT attack followers, or any friendlies in Fallout 3. Even Dogmeat bites back.
Dad: I brought you into this world... you know the rest.
In an NPC example, Ahzrukhal forgot about this trope, as is demonstrated if you buy Charon's contract. Charon may obey whatever command his boss gives him, but he still has a conscience - and once that contract changes hands, he will make his feelings known. So go ahead, nuke Megaton and then tell him he's fired.
Viking: Battle for Asgard: Done literally when Skarin unleashes Fenrir because Freya broke her promise to let Skarin seek entry to Valhalla after killing Hel.
During the climax of Final Fantasy XII, Vayne boasts his own power and makes not-so-veiled threats against his brother, Larsa. Just as the heroes confront him, who would chance to overhear but Judge Magister Gabranth, charged with Larsa's well-being by the late Emperor Gramis, and whom Vayne had treated as nothing more than a hound and a blade to further his own political ascent.
Arguably, this was part of Vayne's plan, Magnificent Bastard that he is. The threat on Larsa at least; earlier cut scenes strongly implied that even with his fratricidal and patricidal history, Larsa was the key to his plan in the end (forge an empire with a bloody war and underhanded tactics, cross the Moral Event Horizon a few times, and leave everything to his young idealist brother who would emerge with clean hands from it all). Vayne's treatment of Gabranth was likely just the way he was, an arrogant jerk.
In Arcanum: Of Steamworks & Magick Obscura, the player can find several half-ogres magically bound to a cruel master in the Dark Elf village. Killing this master will release them, and they immediately turn on their tormentors. The elves never stand a chance.
During Iji's departure from Sector 3 during a Pacifist Run, she will mention the truce between her and the Tasen to Elite Krotera, who goes apeshit and screams about "worthless Vateilika" before announcing his intent to kill her - after Iji herself bites the big one. Krotera, you may Talk to Vateilika's MPFB now.
Vateilika: I've heard enough of that, thank you.
In Odin Sphere, the dragon Belial kills one of the Wise Men that had enslaved him with the last bit of energy he had left.
In Darksiders, Uriel refuses to save Abaddon from War while he begs for her help. Given everything he's done up to that point, Uriel telling him to "f*** off and die" despite her past feelings for him makes perfect sense.
Starting with Crash Bandicoot 3: Warped, Dr. Neo Cortex, the Big Bad of the first two games, ends up The Dragon for Uka Uka, an evil spirit inhabiting a tiki mask, and spends several games fearfully trying to keep the mask pacified. By Crash: Mind Over Mutant, Cortex has teamed up with his old partner N. Brio and captured Uka Uka as the power source for the latest world domination plot.
Cortex:I used to run this show, and it's time I did so again!
In Dragon Age: Origins (specifically "The Stone Prisoner" DLC), part of Shale's backstory is that, after years of ill-treatment by Wilhelm, Shale ended up killing him. There is some ambiguity over possible outside influence however, and Shale claims not to be able to remember the incident. Whether it was intentional or not, Shale's vindicated satisfaction makes it this trope.
Then let's not forgot the great pigeon massacre that is unleashed by Shale after years of being pooped on by birds.
The players can make these happen in Fire Emblem if they so desire, by having the right unit take out the right boss:
In Fire Emblem Genealogy Of Theholy War, taking out Travant with Leif will lead to the latter, usually a gentle young man, screaming how much he wants to kill the first for killing his parents, kidnapping his sister, and leading to the destruction of his homeland.
Fire Emblem Awakening, if Say'ri kills Excellus, she will love doing so since he cruelly mocked her brother's death and the circumstances leading to it.
Fire Emblem Fates, depending on the chosen route, has either Saizo or Shura being very willing to do this to Kotaro, who murdered Saizo and Kaze's father and destroyed Shura's homeland.
In Paper Mario: The Thousand-Year Door, Vivian pulls a Heel–Face Turn because Mario was kind to her in helping her find something that Beldam dropped and forced her to look for as punishment. The next time you face the Shadow Sirens, she can be used as a partner.
Vivian: I'm with Mario all the way! Today, Sis, I am going to punish YOU, do you hear me?
In the backstory, the Ayleids (Wild Elves) of Cyrodiil took the Nedes, human ancestors of most of the modern races of Men, as slaves. As if that weren't bad enough, the Ayleids were needlessly vile in their Dog-Kicking, committing such atrocities as skinning runaway slaves alive then turning their hides into blankets for human children, creating sculptures and gardens out of human bones and entrails, and setting human children on fire then loosing wild animals on them. Their slaves would revolt, and they would eventually drive the Ayleids to extinction as a unique race.
Following the events of the Oblivion Crisis, the Argonians, a long-time Slave Race to the Dunmer (Dark Elves) who were weakened due to the events of the RedYear, took the opportunity to invade Morrowind, the Dunmer homeland. They most of the still-habitable portions, along with Morrowind's rich ebony deposits.
This is essentially the plan for (what remains of the) Third Cyrodiilic Empire against the Thalmor-led AldmeriDominion following the Great War of the 4th Era; bide their time, acting like a weak and obedient state, until it is time to invoke this trope. However, part of "biding their time" involves following the rules set forth by the Dominion in the ceasefire, especially the ban on Talos worship. Being perhaps the most popular god to the Nords of Skyrim, they do not take the Talos ban very well, leading to the Stormcloak Rebellion and Skyrim's full blown civil war. The Dominion is of course all too happy to let the Empire bleed itself dry, hoping the war lasts for as long as possible.
The Dragonborn can choose to help the leader of the Forsworn escape and take his revenge on the man who imprisoned him and used him to make the Forsworn kill for him under the guise of terrorism.
Arondil, a necromancer who uses the undead spirits of young women as sex slaves. Stealing the soul gem from the pedestal behind Arondil's throne will result in two of his ghostly servants turning against him and murdering him.
Imperial Agent: You get brainwashed so that you can't refuse a command by an SIS agent (and being that SIS thinks you're actually on their side, they order you to do things you probably don't like if you're faithful to the Empire). When an SIS agent is badly injured and cannot utter the keyword required to make you fulfill orders involuntarily, you have the option to let him bleed to death and remark spitefully about his condition, thus letting you indirectly bite him back. Later you can free yourself of the brainwashing and kill all of the SIS agents you were in contact with while being a double agent.
Bounty Hunter: If the player back-talks Darth Tormen, he will make a rather unpleasant example of your companion, force-choking them almost to death. At the end of the class story you have the option of making him pay dearly for using and underestimating you.
Subverted in Mass Effect with the geth. In the third game, after witnessing atrocities committed by the quarians during the Morning War, including attacking geth sympathisers, you have the opportunity to let the geth destroy the quarian fleet when the quarians attack them. However, the geth actually have no ill-will towards their creators, and later a geth prime shows genuine regret for being forced to destroy them.
A straight example with Khalisah al-Jilani, who has the opportunity to knock Shepard flat on his ass, in revenge for his decking her twice before.
In Metal Gear Acid 2, Vince was the leader of the security forces at SaintLogic, and attempted to quell the situation at the island and take care of the intruders (Snake and Venus). When he learns that his boss, Rodzinski, is planning to ditch the security forces to take the blame for the Praulia Massacre after the ICC reneigned on the deal, he orders his men to shoot his chopper down.
In Alpha Protocol, there is a sequence in the Grand Finale when you have a dual boss battle with Alan Parker and Conrad Marburg as part of a Timed Mission. However, depending on your actions previously in the game, you may have learned of something terrible that they did to each other, which you can then reveal to one to get him to turn on the other. If you discovered that Madison was Parker's daughter and Marburg killed her in Rome, you can tell Parker and he will attack Marburg, getting himself killed in the process and wounding Marburg just ahead of your fight with him. If, on the other hand, you got 100% of Marburg's dossier and 80% of Parker's before embarking on the mission, you can tell Marburg that Parker was the analyst who hung him out to dry, ruined his career, and nearly got him killed on his last mission for the government years ago. Marburg will knife Parker in the back, and you will face him alone.
Alternatively, you can use some other intel to convince Parker that you've derailed all the scenarios he's made for a new Cold War and he'll decide to save his own hide by selling Halbech down the river. Then, you can use Marburg's dossier and Relationship Values to convince Marburg that Halbech is going down a certain creek without a paddle and he'll bug out as well. In other words they both end up backstabbing their titular boss.
If you consistently annoy Sergei Surkov and find out he was Halbech's Moscow contact you're given the option of sparing his ex-lieutenant Konstantin Brayko (who Sergei had betrayed earlier) and bring him up during your final encounter with Surkov. Brayko will appear and deliver a Gory Discretion ShotExtreme Melee Revenge whose aftermath is described as Surkov having fallen afoul of a rabid tiger.
Narrowly averted in Injustice: Gods Among Us, where after getting grounded for being useless against the Insurgency Lex Luthor Harley Quinn tries to kill Joker. It was thank to Luthor's timely intervention that she put the knife down.
It is played straight in Harley Quinn's arcade ending, though: she breaks The Joker our of jail and decides to marry him, but after he playfuly mashes her face into the cake she finally snaps and murders him with the cake knife.
In Skies of Arcadia, Galcian would have survived having his doom-base destroyed by the heroes and being beaten up in personal combat if he hadn't backstabbed and tried to kill Belleza. Belleza answers his betrayal by ramming his escape pod and killing them both.
In Disgaea 2: Cursed Memories, when a botched summoning causes Etna's levels to sink to 1, her Prinnies waste no time abandoning her. In fact, they fight so hard to avoid her employment that the rest of the party wonders just what kind of Bad Boss she was.
In Disgaea 5, Majorita was singularly raised to fulfill Void Dark's agenda in resurrecting Liezerota, under the false pretenses that she would help create a demon utopia; he only really took her on board because her Overload, which reanimates the fallen as zombies, was key to his design. Suffice it to say she didn't take it well when the truth was laid bare for her.
In Batman: Arkham Knight, Catwoman spends the entire game as Riddler's captive in order to force Batman into doing his challenges and chase his trophies. In her DLC (which takes place after the main game), she infiltrates his personal HQ and not only destroys his robot manufacturing facility but also steals all that's left of his money, putting an end to his supervillain career for good.