As a general rule, we expect that our video game protagonists are fundamentally decent people. Games are structured to endorse that idea, as well; there is a natural tendency for players to empathize with a story's protagonist, and while we realize that some games will have a particularly harsh hero, we assume that they are doing what needs to be done.
But sometimes even an otherwise pure and upstanding hero winds up doing something that is at best morally questionable and at worst downright abhorrent. And this doesn't just happen in games wherein the protagonist is meant to be morally grey or the player is supposed to question their actions. Most importantly, these actions are not options chosen during gameplay; they're just part of the game.
8 Samus Aran Wiped Out An Entire Species
By the time players take control of Samus Aran in Metroid Dread, she is already the last source of Metroid DNA in the galaxy. That's because the second game in the series, Metroid 2: Return of Samus (and its remake Metroid: Samus Returns), is all about Samus seeking out and destroying the entirety of the species after having dealt with them multiple times before, a quest more important to her than her otherwise expansive rogue's gallery.
While the Metroids are an engineered race designed to hunt down the dangerous X Parasites, it is clear that they go through a natural life cycle and the child from Super Metroid forms a distinct bond with Samus. So there are no two ways about this, she wiped out an entire sapient species and then used their DNA to avoid dying to a parasitic infection.
7 Commander Shepard Blows Up A Star System
Players have a lot of options for bad behavior as Commander Shepard in Mass Effect: Legendary Edition, some of which come up in replays, but much of that is optional. What is not optional is the Arrival mission at the end of Mass Effect 2, a post-ending mission in which Shepard realizes that a Reaper invasion is imminent and the only way to delay it is by crashing an asteroid into the nearest mass relay. Unfortunately for Shepard, this means wiping out a star system full of Batarians.
That doesn't mean Shepard can't try to ameliorate the actions, and it is possible to send out a warning ahead of time, but no matter what Shepard does the relay will be destroyed and a huge number of lives will be lost. Even in-game it's referred to as a horrible action and ends with Shepard having to answer for the events on Earth.
6 The Boss Becomes A Galactic Conqueror
The plot of Saints Row 4 is not meant to be taken entirely seriously, but the fact that the opening sequence of the game involves the destruction of the planet Earth is still a pretty significant punch to the player. And while the entire premise of the series is that the Saints are pretty awful people, the endings can take this to an entirely different level.
If the player misses even a single loyalty mission in Saints Row 4, the ending of the game features the Boss taking down the galactic conqueror who destroyed Earth... and then immediately stepping into the conqueror's seat and picking up right where he left off, planning to seek out more planets to expand an empire under the banner of the Saints. It's certainly a major turn for a character who sought revenge against someone doing exactly that.
5 Nier Leads To Humanity Going Extinct
Far more people have played NieR: Automata than its predecessor, the recently remastered NieR: Replicant. It's a major turning point in the former that the human beings the androids are fighting to save in Automata are already gone, but anyone who played Replicant already knew that, because it was a central plot point of the game.
By the end of NieR: Replicant, players are led to understand that the Shades fighting against the protagonists are actually the souls of humanity that have been defending themselves against the eponymous Nier's actions. However, he is undeterred by this revelation which ultimately leads to the complete extinction of humanity to fulfill his own quest to save his sister.
4 James Sunderland Is A Murderer
Silent Hill 2 is lauded by many game critics and fans alike as being one of the high points of the series as a whole, a descent into horror in the depths of a mist-filled town. But while later entries such as Silent Hill: Downpour would make a point of giving players morally ambiguous characters as the protagonist, Silent Hill 2 also gave us a protagonist who was indisputably guilty of an awful crime before the game even began.
James Sunderland came to the eponymous town of Silent Hill after receiving a mysterious letter supposedly from his deceased wife, Mary, but James himself was responsible for killing his wife to spare her further suffering from an unspecified disease. At the time she was suffering from severe mood swings due to her illness, but the guilt James feels from having caused the death of his wife is also directly responsible for the horror that unfolds around him.
3 Cloud Gives Sephiroth The Means To Fulfill His Plans
With Final Fantasy VII Remake still fresh in everyone's mind, few are likely to forget about Final Fantasy VII's overarching story any time soon. But even as the remake is poised to change some elements, it's worth remembering that in the original game Cloud literally hands Sephiroth the Black Materia, the key to Sephiroth's plans, on two separate occasions.
The first time the party seeks the Black Materia, Cloud is manipulated into giving it to Sephiroth, which directly leads to Aerith leaving the party and ultimately being killed by Sephiroth. Much later, the party recovers the Black Materia... at which point Cloud once again is manipulated into promptly giving it away, making him directly culpable for all of the destruction and danger that Sephiroth unleashes.
2 Joel Murders For Ellie And Lies About It
For much of the run of The Last Of Us, Joel is clearly driven to a savage intensity to keep Ellie safe from both humans and horrifying monsters. He doesn't hesitate to kill, but his hope that keeping her safe and reaching the Fireflies will lead to a cure justifies a great deal of what he does. It's only when it becomes clear that the cure will ultimately involve Ellie's death that Joel shows his true colors, murdering the people trying to research the cure in large numbers with just as much viciousness.
What comes next is what really cements his actions, though; when Ellie asks what happened, he lies and claims that they simply left because the Fireflies were no longer seeking a cure. While the sequel explores the consequences of these actions, The Last Of Us is clearly meant to raise difficult questions about the justification behind his actions.
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V Ruins Clouds No Matter The Choices
One of the recurring themes in Cyberpunk 2077 is the difficulty, if not impossibility, of making big changes on a systemic level in Night City. This is in stark contrast to the game's own post-launch changes from ongoing patches to a well-received tie-in series, not to mention how easy it is to modify weapons to be better. The line of quests that center around the treatment of the dolls working at Clouds drives this home, with V ultimately having four options to resolve the line... all of which make the situation worse.
If V chooses to work with the ambitious Tyger Claw member, Maiko, who seeks to take over the club's management, she proves to be just as bad as her predecessor and leads to working conditions being just as awful as before. If, instead, V chooses to oust the Tyger Claws altogether and declare Clouds to be run by the workers... the Tyger Claws come back and retaliate with force, killing some of the workers and forcing others into hiding. No matter how this mission resolves, ultimately, things get worse for the people working there.