In Anachronox this trope gets played on the player as well. After freeing Paco, a native tribal elder figure tasks you with finding four golden leaves of ritualistic value to proceed. Options are numerous. You find some lying around or growing on plants, collect silver as well to exchange for gold, collect berries to exchange for leaves, refuse giving up what you found for charity. But you just can't get four unless you steal some, and/or unless you spoof some unripe berries for ripe (you are aware that unripe ones cause sickness). If you refrain from resorting to ill means and naturally come up short, you can report back to note a dialogue option that you "can't find any more." It gets accepted! You proceed. Once out of the gate, you won't find a difference in the rest of the game.
The Elder Scrolls series frequently provides opportunities of this nature for the player. Perhaps you find yourself alone in the home of an elderly widow and her life savings are sitting there unguarded... or maybe you run into a lone traveling merchant out in the wilderness... no one would ever know. Plays into Video Game Cruelty Potential and Kleptomaniac Hero significantly.
In Grandia II, Ryudo is sent to prove his worth to become the next super-powered-being to defeat the 'evil Valmar'. Along the road he is questioned and every answer he gives is twisted to be perceived as a selfish desire. The next shot has him in darkness transformed into a demon with a voice telling him to embrace it. However thanks to the The Power of Friendship he's freed and ends up with the sword to defeat evil.
In Neverwinter Nights, the canonical Player Character fought hard to prevent Aribeth's execution, despite the fact that the entire leadership of the city was arrayed against him and Aribeth's state of mind made her believe she deserved it.
In Betrayal at Krondor, the dark elf Gorath's initial act of joining the humans to prevent the war his people are planning against them qualifies. He knows in advance that it will strip him of his rank as chieftain, that his own people and what remains of his friends and family won't consider him anything more than a traitor and a coward for thinking of cooperating with humans, and the humans themselves will at best distrust him and at worst have him deliver his message on a rack. He goes anyway.
In Persona 3, during the month of December the Player Character and party are asked to decide whether to try to fight against the supposedly unstoppable End of the World as We Know It, or to kill Ryoji, the avatar of the embodiment of death, which still won't prevent the Fall but will erase their memories of everything related to it and thus allow them to live out their remaining few months in peace, unaware of what's coming. Each party member separately resolves for themselves that they'd rather fight, but the ultimate choice comes down to the protagonist, and if you choose to go against the rest of the party's decision and kill Ryoji, nobody will ever even remember that it was an issue. Unsurprisingly, doing so leads to the game's Bad Ending.
In Persona 4, a crucial decision late in the game is centered around this. A loved one has just passed away and you and your friends are in the same room with the person responsible. You have the option of murdering him by throwing him into the TV, with the knowledge that no one would ever find out that you were the ones who did it. Of course, just like in Persona 3, this leads to the bad ending. Instead, it's staying true to your principles (you are the Investigation Team, and you swore to get to the bottom of the case and find the real culprit) that puts you on the road to the good ending.
Persona 5: The Shadows selves in the hidden Mental World of the Palace represent the twisted secret feelings of the respective adults you target. Similarly, when characters' Persona first awaken, they encourage their other selves to ignore society's expectations and unleash their true rage / vengeance / etc. on those who have wronged them.
On a darker note, Big Bad Yaldabaoth gives the protagonist a choice near the end: continue to fight back against a god who has already written him out of existence once, or join forces with Yaldabaoth and use the Metaverse to control the world. Doing the latter gets you an ending in which the protagonist has become a Knight Templar ruling Tokyo through fear and brainwashing, while rejecting Yaldabaoth's offer lets you save your friends and the world. It's implied that the hero rejects the offer on principle; he's not going to go back on everything he's done and become the monster he's been fighting for any reason.
Morgana, a cat, tries to fight off Haru's rapist. He knows there's no chance of his little scratches making any difference, but anything that delays the crime and shows Haru she is not alone is worth it.
Coldly discussed by Tayama in Shin Megami Tensei IV. To him, humans are so weak, no one ever chooses the higher moral option in the dark. This means he views his totalitarian regime, backed by Yakuza, as entirely in everyone's best interests; by forcing everyone to cooperate to help each other, even in the face of the monstrous acts he and his organization commit, he is indeed improving the life of everyone.
In Splinter Cell: Chaos Theory, Sam Fisher is tasked with destroying the wreckage of a downed US plane by calling in an air strike in order to prevent sensitive information from falling into enemy hands. He has the choice whether to spend precious time carrying the two unconscious pilots to a safe distance first or not, and doing so causes a new guard to spawn and happen upon him at a very inopportune moment (as when carrying a person Fisher cannot use any of his weapons). However, if he chooses to do so anyway he is confronted with this trope by his superior.
Lambert: You don't even exist Fisher, you can't get a medal for this. Fisher: Medals don't help me sleep at night.
SOMA drives the main character in its entirety through moral dilemmas with a very dark tone, almost always alone in the choices.
At the beginning, the main character, Simon, must restore a power generator in order to activate a security computer and unlock a door. Inside the room there is also a mauled talking android who refers to himself as Carl Semken (whose artificial brain has a digital copy of the mind of the real Carl). However, if you activate the generator, you will necessarily electrocute the android, which is plugged to the power line. He will scream in extreme pain asking you to stop the process, which you can do. If you don't, he will forever continue to painlessly scream while you continue through your tasks. If you do, Simon will apologize for pulling the wrong switch and the android will not mind. But if you let too much time pass before stopping electricity, and you try to talk with him again, he will be agonizingly speechless because you fried his circuits. Alternatively, you can follow an alternate path that will lead you to reroute energy from the room to a secondary computer that you can use to override the security locks of the door. This however will kill the android as no energy will flow anymore in him (and will also unlock another door that spawns an enemy). Both paths lead to the same destination.
When the player reaches the shuttle transit system of the facility in order to get to Site Lambda, it is discovered that it lacks energy too. The power generator is in a nearby room, attached to a suffering woman. She's mantained alive thanks to a sort of black biometallic mass, that plugs her body to artificial lungs powered by the generator. She states that this condition is of heavy suffering and "it won't let me die". There are two power nodes. If the player unplugs one and reconnects with the transit system, the generator will allow both the artificial lungs (although the woman will suffer even more) and the shuttle to operate, but the security program of the transit system will be marked as unstable. If both nodes are reconnected, the woman will die but the security system will be safe (actually, no matter the choice, your shuttle will crash anyway for the plot).
At some point, the player will need a power battery to restore energy to another transit system in order to reach a site called Theta. There are only two possible sources of a battery: either A) a patrolling, apparently crazy robot, which talks to himself and responds to the main character with nonsense answers (because it hosts the brain scans of two different people), or B) a small assistant robot, referred as "little guy" by Simon, with an intelligence stated to be as that of a dog, which the player rescued before from some blocking rocks, and which in turn helped him to cut open some armored doors following him as a sort of friend for a while. The player must kill one in order to retrieve the battery. However, if the player chooses to kill A, the assistant robot will change attitude, displaying fear and stepping away from Simon if moving nearby. Although techically a robot, moreover with an intelligence comparable to that of a dog, it could be disputed that this choice is not done while being true alone and without judging witnesses.
During mid game, before entering Theta, the player will meet another mauled robot with a female voice, introducing as Robin Bass. She can't move as the robot doesn't have any legs and is severely damaged. She will wonder where is anybody and if she reached her scheduled destination ( she is a digital copy of the mind of the real Robin Bass, supposed to be uploaded into a machinery called "The Ark" which hosts a virtual paradise where brain scans of last surviving humans dwell in peace). If the player talks with Robin for a while, Simon won't tell her that everything is lost and the people she knew are no more there, instead lying about her condition. After that, the player may notice that it is possible to interact with a power node from Robin's metallic body, thus unplugging and "euthanizing" her. Alternatively, the player can walk on, leaving the robot literally forever alone in a nightmarish setting, without any way to even move or suicide. Both choices don't affect the subsequent path of Simon.
After this part, the player will need to interact with a digital copy of a former technician of the facility inside an hard-disk, in order to retrieve a passcode. After obtaining the pass, the player can choose to erase all the data from the hard-disk, if desired. This has no effect on gameplay, and it's only a moral choice whether the digital copy of a brain is considered an actual person, whether it's right to leave a brain scan in a perpetual limbo inside an hard-disk until someone powers it, and whether deleting it is killing.
In the same section, Simon will discover the template of HIS digital brain scan, which could pe potentially used to create more copies of his mind (although there is nobody who can do that). The player might choose if erase the data from the computer or let it be. Both choices don't affect gameplay.
Towards the ending, just before leaving Omicron, Simon will need to assemble a new cybernetic body with an advanced environmental suit, in order to transfer his mind into it. However, he discovers that his mind wasn't transferred, only copied, thus there are now two Simons inside two different bodies. Catherine disables the first one, and Simon protests that she lied and the other body will awaken alone in a living nightmare, which is "so cruel". Then Simon suggests "what if he doesn't have to wake up at all?". Before disconnecting, Catherine leaves to the player the choice whether unplug the previous Simon, who will die in less than a minute after exausting his internal battery or proceed without doing anything further. The choice doesn't affect following playthrough.
In Thief: Deadly Shadows, at the end of one level, you find a secret stash of gold left by late Captain Moira for his wife. It's a pretty penny and you don't get any penalties later in the game for taking it. In fact, your only deterrent is a brief popup message "Mrs. Moira needs that money to survive" but logic tells you that she probably won't find the stash in her current condition anyway (you meet her earlier in the level: she is utterly broken by grief). So, that's the point where you learn what you are in the dark. Garrett doesn't make any comments either way.
Sadly the loot requirement on the highest difficulty level makes completing the mission impossible without taking the gold.
There is a minor deterrent to taking the loot: The following night, a thug loyal to the widow can be found skulking in front of the door to Garrett's apartment building, looking to avenge the theft. He's just another Mook, however, and not much of a threat.
And they ask, What is a Hero? though the answer is very clear, He is the one who faces danger when the darkness hovers near. He will face the fiercest foe when another needs his aid. He will dare to defy Death even though he is afraid. He works not just for glory, and he does it not for gain. But because he knows that others will be spared a greater pain.
The second game was the part of the series where the designers introduced the tests of character. While some actions are obvious (don't kill the guy you're fighting just to get approval from the Eternal Order of Fighters), some are very much less so (while racing to save the world from the destructive power about to be unleashed and you successfully disarm the Dragon blocking your path, you can kill him and no one will ever know, and in fact will probably praise you for going as fast as possible...but you'll know that you killed an unarmed, helpless man). Later games made the choices a bit more obvious, but there are some surprisingly ambiguous decisions.
In true keeping with this trope, there's never any real reward for being 'good' about it. Meanwhile, the reward for being evil is sometimes impressive...so, just how 'Grey' ARE you, Warden?
The Desire Demon possessing Connor. The wholly right and moral decision is to refuse any deal and fight the demon/scare it into leaving for good. The only reward is some experience and whatever loot it drops. What do you get for agreeing to the deal (if playing as a mage)? The only chance to unlock Blood Magic. And the only ones who would know either way are you and the demon. Though in that case there is another choice: if you have Master Coercion, you can intimidate the demon into bribing you to let her leave without a fight.
However, unlocking a class in Dragon Age: Origins permanently unlocks it for every playthrough regardless of the decision. There is nothing preventing you from unlocking it and then immediately resetting it and resolving the quest in a different way. In addition, the Awakening expansion adds a manual that unlocks it.
The game's most pivotal moment. You find out that the Grey Warden who kills the Archdemon must die with it, but Morrigan privately offers a way out through Deus Sex Machina, and absorbing the Archdemon's soul into the baby conceived. However, she refuses to tell you what she plans on doing with the child afterwards. Dragon Age: Inquisition shows that she actually makes a pretty good mother, and if the player romanced her and went through the Eluvian at the end of Witch Hunt he sticks around for a while to help raise Kieran.
Mega Man 7: Rock has beaten Dr. Wily again and Wily starts to beg like normal. However, by this point, Rock has had enough of Wily and remembers all the pain he caused the past six games. He begins to charge his buster and says he's going to do what he should have done years ago. Wily points out that robots can't harm a human being. While the US version has Rock declare he's more than a robot and looks like he'll do it until the fortress self destructs, the Japanese version has Rock pause long enough for the fortress to collapse.
In Dissidia 012 Final Fantasy, Kain Highwind is a morally ambiguous Anti-Hero who has spent the story up to the final tale killing off his allies (or as the game says, "puts them to sleep") so that they'll be safe when the cycle of war begins again, rather than risk them fighting and dying against the new threat of the Manikins. Needless to say, no one is very pleased with him over this and several don't trust him even as he accompanies them to the portal the Manikins are coming from to help them close it. Along the way they're stopped by Exdeath and a group of Manikins and Kain stays behind to hold them off while the group continues on. In a bonus scene, Golbez approaches Kain afterwards and tells him that if he goes to join his friends in their Last Stand, he'll die and no one will remember his bravery. Or he can stay behind now and live to the next cycle, and again no one will know. Kain goes to help them.
Kain says "put them to sleep" because once everyone on one side dies, all deceased fighters are resurrected and the fight starts over. Unless you die fighting Manikins.
Mass Effect gives this to the last survivors of its Precursors, the Protheans. The last dozen or so sapients in the entire galaxy work feverishly for decades to reprogram the Keepers, seemingly benevolent drones who are critical to the Reapers' cycle of galactic extermination. Then they take a one-way trip to the Citadel, the key in the Reapers' trap and the center of galactic civilization. Without food, water, any ability to sustain a breeding population, or anyone to judge them, they faced a grim death from starvation so future generations of sapients could avert the disaster that destroyed their civilization. And the Council denies their existence. But Shepard will kick ass, take names, go to hell and back and shake hands with the Illusive Man himself to make sure it was not in vain.
Still in the first one, this trope is invoked when facing a Deadly Doctor who Garrus has been after for a long time. You can choose to gun him down where he stands, or try to apprehend him, at which point he charges at you and you have to kill him anyway. Garrus asks why you bothered arresting him, since he died anyway, but Shepard counters that it's the trope that counts; that they still tried to follow the law.
The whole of Mass Effect 2 is like this, since 99.9% of the galaxy thinks Shepard is dead. Happens to Shepard him/herself in the ArrivalDLC. You have a choice to warn the batarian colonists that they have to evacuate, or just contact the Normandy. The choice itself has no real consequences (the warning communication is blocked anyway), but at the time, Shepard could conceivably be sacrificing him/herself for three hundred thousand civilians. It's arguably even more poignant if Shepard is from Mindoir.
Jacob lampshades this trope when telling Shepard about his proudest career moment, which the Alliance covered up for the sake of not inducing a panic. He's comfortable with it, though.
Jacob: Good deed's like pissing yourself in dark pants. Warm feeling, but no one notices.
Jacob's father faced a situation ten years before the game that occurred in relative "dark". The ship he was serving on crashed into an unknown planet in the ass end of the galaxy, killing the Captain. Being the First Mate, Jacob's father took over, with the help of other officers of the ship. The short version is, it did not end well.
Mass Effect 3 has this with the offer that the Salarian Dalatrass offers you regarding curing the Genophage. However depending on which party members survived previous games, your decision can become public, with unfortunate consequences if you took the Renegade path. If the characters needed for the renegade choice to backfire aren't still alive the situation is different enough for the morality of the choice to be a lot less clear-cut.
The end decision in Mass Effect 3 can be seen as this if you pick the Destroy option and are implied to survive. After all, with all artificial life in the galaxy destroyed, including EDI and the geth, there's no one else alive who knows that Shepard was informed of the consequences of the action and did it anyway. The entire choice is very much What You Are in the Dark: it's about which principle Shepard most wishes to uphold (or, conversely, is most loathe to throw away) when faced with an explicit choice and absolutely no oversight — whether they most want to end the war cleanly, take control of the most powerful force in the galaxy, usher in a new and unforeseen era of existence, or go down spitting defiance to the last breath. Even better, you can justify each decision as the moral "Right" and "Wrong," so the decision is entirely up to you. Bioware doesn't tell you which one is right.
In Space Quest I, upon encountering the Sarien ship that massacred the Arcada's crew and has the Artifact of Doom that they are going to inflict on the galaxy. It's a massive ship full of hostile aliens, against one not-so-Almighty Janitor. The pilot droid wisely suggests hauling tail. It's Non-Standard Game Over if you take him up on it.
Pablo: I've got more money than you've ever seen! What say you? Join me, and take a seat of power at my side.
Occurs in the flashbacks of L.A. Noire. After returning home from Okinawa, several Marines were upset when they saw stories that Phelps was the LAPD's Golden Boy, and resolved that since they had been denied fame and fortune, they would take it by stealing the supplies on the boat they were returning on. One character notes that they can get away with it and do good, but another character (who they all respect) tells them that he will not stop them, but if they actually do it, they are dead to him. They fail the test.
Touhou: Reimu Hakurei has to take this in stride. Solving more prominent incidents like the Scarlet Mist (Embodiment of Scarlet Devil), vengeful geysers (Subterranean Animism), and the earthquakes (Scarlet Weather Rhapsody) are things she can probably make realistic claims about; but, in general, no one really knows about most of Reimu's efforts to keep the peace in Gensokyo and one of the two (known) reporters in Gensokyo tells her to her face that she has no concrete proof of any of her glories. (Her grouchy attitude when she's off solving incidents doesn't help matters, either.) Hakurei Shrine getting no visiting worshipers is canon.
In a tongue-in-cheek sort of way, the fan-made list of Touhou games described as atrocities caused by Reimu lampshades this problem.
The Bard's Tale has this for the ending, where the Evil ending where he sides with the Demon Queen to enslave the world is the Bard's personal happy ending while the Good ending has him save the world but starting back where he was at the beginning as a poor conman. Alternatively, he can just walk away and party with the zombies.
Star Trek Online has the mission Operation Gamma, where your player captain is abandoned to die by a Ferengi captain who was supposed to guide you to the Dominion, only for her to end up fleeing right into the arms of a Dominion force. When your ship arrives, the Vorta in charge of that force declares that by their logic they should kill you both for trespassing, but since you'd actually been looking for them in the first place, he offers to help you — if you kill her. The mission progresses either way with only a slight difference in NPC dialogue, but if you kill her, the Vorta declares, "Now I see what kind of officer you are..."
In Hajime Saito's route in Hakuouki, the trope plays out complete with stock dialogue in a confrontation between Saito and Kazama. Saito is hopelessly outmatched and grievously wounded, and Chizuru tries to save him by turning herself over to Kazama, who smugly suggests that Saito can tell his superiors that he tried to protect Chizuru but was overpowered. Saito retorts that he would know, and that he doesn't surrender to anyone.
FTL: Faster Than Light doesn't have an explicit Karma Meter, but many events will test your morality. Do you take the bribe of a pirate and let him go after some ship, or do you take him on? When a slaver offers gifts in exchange for letting them live, do you accept and let him live to continue his dirty work, or do you finish the job? Do you help when asked for it, even if it may cost you health, ammo or crew? There's no one around who will judge you, only your conscience. Choose, skipper.
During the final part of Grim Fandango the protagonist, Manny Calavera, finds himself alone at the Number Nine train station, where he can approach the Tunnel to the Ninth Underworld. He briefly muses that he could just walk through it (which he technically has the right to do at this point - his adventures do count towards the four-year journey that the less "saintly" souls must complete before they can leave the Land of the Dead). However, he promptly refuses to do this, because there are still other souls in need of his help. Considering that getting out of the Land of the Dead was Manny's initial goal (a goal he was willing to achieve by stealing a client from a fellow Reaper, which is how the whole mess started), that indicates a pretty strong Character Development.
In an odd variation, Manny receives a Golden Ticket for the Number Nine as reward for services rendered - though he no longer needs one.
In The Sims 3, if your character is in the political career track, he/she can choose to steal funds from the campaign fund when given the opportunity. You will not get caught.
In the first installment, Rufus is given the option to take over Cletus' life, including Goal. Instead, he decides to save a planet full of trash and people who hate him.
In Chaos on Deponia,Rufus owns up to a major lie, knowing he might lose Goal by doing so.
Comes to a head in the finale of Goodbye, Deponia, where in order to prevent Goal from dying and make sure Elysium is informed that people are still living on Deponia, Rufus claims to be Cletus, justifying it by going on about how selfish and unchanging Rufus is, and finally dropping from the highboat and falling to his death.
For reference, an article reports that the majority of players try to do the right thing, even if it makes less sense from a logical perspective. They also report on subtle decisions, such as players stopping an action once they're being watched.
It's not quite "in the dark", though. The player character becomes the de facto guardian of an impressionable small child very early on. It's played straighter in the sequels where she's the player character, but even she picks up has her own wards pretty quickly.
In The Godfather II, the sidequest targets you can choose include both scum who deserve some Pay Evil unto Evil and good or otherwise normal people who the questgiver wants harmed. There's no explicit Karma Meter or ingame consequences, though, and no one will comment on whether you choose to play the Vigilante Man, be the villain or do some mix of the two because It Amused Me. All up to your conscience, signor.
Shown during a cutscene following the final heist in Grand Theft Auto V. The armoured car driver they threatened into assisting with the heist has to be dealt with. Trevor, of course, wants to shoot him because he knows too much. Michael tosses him a bar of gold, pointing out that if he takes it, he's now part of the robbery and has as much to lose as the actual thieves, so it's in his best interest to keep his mouth shut. The guard takes the gold.
This trope could very well be the Central Theme for Dishonored. The Outsider gives selected individuals his mark and lets them do as they please with the new powers they have. Most people are shown to use their powers for self-gain, and becoming deeply corrupt and insane as a result. Corvo gets the mark early on, and it's up to the player to either use his powers to easily cut a swath across the city and murder all of his targets, or to hold back his violence and preserve as many lives as possible. Doing the former will inevitably lead to the downfall of Dunwall. This plays into the Daud DLC as well, with The Outsider even saying that no one but him will ever know the story of how the Knife of Dunwall stopped the Brigmore Witches from possessing Emily.
This theme extends beyond the Outsider's marked. Pretty much every character in the game goes through their own tests of character, from the Lord Regent to Admiral Havelock. Most of them fail.
A major theme and gameplay mechanic in Papers, Please. Do you go about your job and assess the passports of the people trying to get into Arstotzka to the best of your ability in order to pay rent and support your family, or do you try to show sympathy to the prospective entrants and bend the rules where possible, even though doing so will incur punishments? Or even worse, do you have as many people arrested by the security guards as possible, given that doing so carries significant financial incentives?
Like its inspirations Heart of Darkness and Apocalypse Now, Spec Ops: The Line is in large part an examination of how ordinary people behave when the civilizing influence of orderly society is absent. The game goes a step further by drawing an implicit comparison between how the average person would act in such a situation, and how a typical gamer behaves while playing a shooter.
Occurs at the end of Bastion, when The Kid is deep in hostile Ura territory, and not even Rucks the narrator knows what he's up to. When he finally obtains the final shard needed to power the Bastion, he runs into Zulf, who sold him and his friends out to the Ura, getting beaten to death by his former partners-in-crime for bringing The Kid there. The player then has the option to either leave Zulf to die and take on one final squad of Ura archers with the Battering Ram, or abandon the Battering Ram to carry Zulf to safety, leaving him utterly defenseless against the aforementioned squad.
The protagonist Cole in inFAMOUS is faced with this in the second to last mission when finally having tracked down the Ray Sphere ( the device that gave him his powers and if activated again will make him twice as strong) and is presented with the choice to activate it and gain more power at the cost of probably thousands of lives or to destroy the Ray Sphere for good.
A Side Quest in inFAMOUS 2 involves guarding a prisoner while the cop who arrested him goes to get back up. The prisoner quickly demonstrates that he deserves to have been arrested, and it's up to the player to either let him live to face justice (Good Karma) or kill him and claim he was escaping (Bad Karma).
In the game Injustice: Gods Among Us, we see an Alternate Universe Superman have the choice of killing Joker for causing the deaths of Lois Lane and his unborn son, or let him live. He chooses to kill the Joker, leading him to believe that killing villains will solve the world's problems. He later kills other superheroes who begin disagreeing with him, crossing the Moral Event Horizon.
The entire plot of Life Is Strange is hinged on this. In episode 1, Chrysalis, you have the choice of reporting Nathan, an extremely wealthy boy whose family practically own the school, twice, though both decisions may not work favorably to Max. Other minor decisions can also be made, like whether to prevent a girl from being hit in the head.
Kyuu faces this choice in Chapter 5 of Rakenzarn Tales. He can either stay home and forget about this adventure or go back to Rakenzarn and save everyone inside. No points for guessing which leads to the Bad Ending.
This combined with Save Scumming is played with in Undertale. It's an especially meta example since no one is offering to let you undo mistakes by resetting (like killing Toriel when you were trying to spare her); it's just a convention of games that have save points. Do so, however, and Flowey will chew you out over it, showing that you weren't really alone when you made that choice, and even if no one else remembers it, the two of you will.
If you complete a Genocide Run, your Save file will become permanently tainted, making you unable to legitimately reach the Golden Ending ever again without having "Chara" assume control and kill everyone... You made the choice to kill them all in the first place, and no matter how badly you may want to escape the consequences of your actions, no matter how much good you may dedicate yourself to doing in order to make up for what you did, one person will always know that you let your completionism get the better of you, and they will always judge you for it and remind you of what you are in the dark... And that person is, regardless of what nameor shape they may assume, You.
In Starcraft II Heart Of The Swarm, Kerrigan could have easily let her zerg swarm kill the wounded Dominion soldiers that were retreating from Char after she herself had just killed General Warfield. Kerrigan could have easily justified it as not leaving anything to chance (which wouldn't be unprecedented for her since she had previously murdered the entire crew of a Protoss warship for the sake of survival). Sure Warfield had told her that the wounded soldiers would not pose anymore threat to her, but it's not exactly easy to just trust the word of an enemy commander. However, she instead chose to stop the pursuit of the wounded soldiers, allowing them to live. This action reflected Kerrigan's Character Development from a Villain Protagonist who only cares about her Roaring Rampage of Revenge into someone more heroic.
In Overwatch comic A Better World, Symmetra watched at how far her company Vishkar would go to attain dominion over Rio. She has tried as much as she can to subvert their orders within their surveillance, such as her anti-killing policy, and she'd still let Vishkar know that. But the moment she saw the girl she just befriended in danger of dying from the fire, she proceeded to save her life even when it's more convenient and in-line with Vishkar's Knight Templar zealotry to just leave her to die. Nobody, not even Vishkar knows this, except that little girl, who's ambiguous in either hating her or still believing her out of gratitude. And hell, the world wouldn't know either, to them and especially Lucio, Symmetra would be just a Vishkar cheerleader/golden girl that embodies all its qualities and corruptions (especially the latter) and she would act accordingly to its image of trying to support Vishkar and harassing its oppositions, but the event is considered the definitive reason why Symmetra is theToken Good Teammate and Noble Top Enforcer of Vishkar instead of being the same as her co-workers.
The final sequence of Ending E in NieR: Automata gives the player a choice in this regard: You've just beaten an incredibly hard Mini-Game Credits to finally get a glimmer of hope in the game's world after everything has gone to hell, and chances are you likely did it with help you accepted from other players online after you died too many times to the minigame. Pod 042 reveals that the reason that those players were able to help you was that they sacrificed their game's save data after beating the game to give help to some other random person trying to win, i.e. you. You are then given the choice to do so or not. No one will likely ever know who you are, since you're just a random anonymous name among the thousands in the network; the only satisfaction you will likely get from doing so is your own personal conscience.
Dead Rising 4 takes place 15 years after the original Mall outbreak and features Frank West, now in his 50s, who is no longer the decided and eager reporter looking to break important stories to help mankind, but a cynical, angry, and disillusioned school teacher who no longer believes in doing that right thing, but doing what it takes to survive. This is because of the years he watched as evil people and groups got away with causing the outbreak without any punishment. After a student of his talks him into investigating another conspiracy dealing with the zombie virus, he slowly gets his passion he once lost back, and by the end of the game, once again becomes the Frank West who cares again.
Happens toward the end of Cuphead. When Cuphead and Mugman finally face the Devil in the final level, they are given the choice to hand over the soul contracts they collected from defeating every boss to the Devil and join his side. Now, Cuphead and Mugman owe nothing to these bosses who were probably not very good people, and they would benefit greatly by becoming the Devil's henchmen, but refusing the Devil's offer leads to the brothers instead burning all the contracts and saving all the bosses from having their souls taken away.
In Dark Souls III, Greirat the thief will die if you send him on a pillaging run into Irithyll of the Boreal Valley unless you send either Siegward or Patches to save him. To send Siegward, you have to buy all the pieces of his armour set from Patches (who stole it) and return it to him. To send Patches, you have to not buy even a single piece of the set. No matter who is sent, Greirat will credit his rescue to Siegward upon his safe return. The implication is that Patches dressed in the armour and pretended to be Siegward because he didn't want his reputation as a no-good scoundrel tarnished by being seen doing a good deed, even by/for the one person he actually likes. Indeed, when he first asks where Greirat has gone off to, he immediately tries to play it off as being interested in looting his corpse, though his concern for Greirat's safety is audible in his voice.
The DLC expansion packs have Slave Knight Gael, who might be the greatest example of this trope imaginable. Gael, after a life of grueling service as an undead slave knight, killed over and over only to be resurrected and sent back into the fray, was kept sane throughout his ordeals only by pure willpower. As a decrepit old man he journeyed to the literal end of the world, having taken the long way to the far future, to fetch the blood of the Dark Soul. Along the way he braved all of the hazards of the Ringed City and the transitional lands, and racked up such a body count that the pygmy kings know him as "the Red Hood." He went through all of this after thousands of years of combat and misery solely so that his "niece", the Painter, could use the blood of the Dark Soul to paint a new world, ensuring that there would be hope at the end of the main dying one. His soul description states that he knew he was not going to withstand the corruption of the Dark Soul. He fully expected to be driven insane by the process of harvesting it, and he expected you to be the one to put him down, retrieve the blood of the Dark Soul, and return it to the Painter, even leaving helpful signs to guide you to him. When you finally do find him, slay him, and take the blood back to the Painter, you don't even have the option to tell her where it came from. Gael effectively saved all life, yet there will be no memorials to him, no legends passed down about his deeds, no grand songs written about his life, just a world whose survival was ensured by his quest... and that is enough for a nameless undead.
As the Ashen One, you can choose to invoke this yourself when the Painter asks your name, intending to name the new world after you. Instead of giving it, you can potentially respond that you have no name, causing the Painter to comment that neither does she. Thus, she decides to name the painting "Ash" in lieu of any other option. The Ashen One was indispensable to this world's creation and accomplished many notablefeats besides, yet passes up on the chance to be remembered for it, much like Gael.
Halo 3 has Mendicant Bias, a ForerunnerContender-class Ancilla designed to beat the Flood. It ended up betraying the Forerunner after the Gravemind managed to convince it. Another AI, Offensive Bias, managed to beat him and imprison it in the Ark for 100 000 years as punishment, where it spent time wishing to atone. It eventually saves the lives of the Master Chief, the Arbiter and Cortana when the replacement Halo ring and the Ark are severely damaged at the end of the game, and the only way you'll know about it is if you read the last terminal on Legendary difficulty.
One moment in Call of Duty: Modern Warfare (2019) lets you choose between letting a known terrorist (who callously murdered a child in front of your eyes earlier in the campaign) live or getting revenge and killing him in front of his wife and son. Regardless of the outcome, the protagonist in the situation does question the methods but it's ultimately your choice as a player in that moment.
Lieselotte: Hmph. So much for the saintess... Call you what they will, this is who you really are. My dear Rosea... I believe...at last...we see...eye to eye.
Star Wars: The Old Republic: Jedi Knights will have their morality tested at the end of the Prologue. After defeating BengelMorr, Knights will have the option to either 1) spare him so that he could be redeemed (light side), 2) kill him (dark side), or 3) let him leave unredeemed to "prepare the galaxy" for themnote since he believes the Knight to be a Dark Messiah variant of The Chosen One (dark side). Your actions won't be immediatly found out due to the fact that the only other beings present during the encounter are the Knight's Master, who is unconcious, and T7-01, who is a droid and thus can have its memory wiped.