Amnesia: The Dark Descent is an odd example. The backstory, which is slowly revealed over the course of the game, shows that the protagonist was once a normal man who sunk to shockingly low depths in order to save his own life.
In the sequel, Amnesia: A Machine for Pigs, the big twist is Mandus is responsible for the machine's creation and his sons' deaths. A part of his soul is part of the machine and it was trying to purify the world based on his creator's, Mandus's, intention. The ending does fix this.
Mortal Kombat games usually allow you to play as some of the villains (Shang Tsung, Shao Kahn, Quan Chi, Shinnok, etc). Winning the game as them shows what happens when the bad guy wins.
Armored Core For Answer is mostly Grey and Gray Morality, but one of the endings has you and a psychopathic cohort go on an Axe-Crazy murder spree that leaves millions dead in the span of a few hours. The final mission involves the two of you fighting everyone left standing that can oppose you, including your own com operator, all at once. They managed to kill your cohort, but fail to kill you. It's hinted your unchecked rampage sends humanity right back to the dark ages.
Neverwinter Nights 2: Mask of the Betrayer bears mention, because there is no other clear villain in the story unless the player takes it upon him or herself to be one. It is hard to consider The Founder a villain, despite what she did, and the only other character who bears any blame has been dead (for certain values of dead) for centuries.
Still, if you consider Donkey Kong the villian of the old games (and definitely of the Mario vs Donkey Kong games), Donkey Kong Country could be seen as this (Though, Donkey Kong definitely is the hero in DKC).
The unnamed protagonist of Hatred is a ruthless Misanthrope Supreme with the goal of dying while taking as many people with him as he can.
Overlord, although you're allowed to choose between being really evil and just self-proclaimed evil. Plus, given that all the "good" characters are corrupt, choosing the latter option makes you the most sympathetic character in the game with this depiction being decidedly canon (the Overlord at least saves the Elves and Rose is the mother of his child). In the sequel you are 100% evil and you fight some genuinely Good foes, though your main enemies are still the anti-magic Glorious Empire bent on the destruction of all magic. Lord Gromgard of the Wii prequel Dark Legend is portrayed as a Villain with Good Publicity who is at the least well-liked amongst his servants for not letting them starve.
The original Grand Theft Auto allowed you to choose your player character from a roster, which had both males and females, but all of the said "characters" were completely devoid of any personality. Grand Theft Auto 2 was the first game to have a singular main character, but even he had absolutely no development.
In Grand Theft Auto III, the protagonist was not even named, and appeared to be doing what he did solely to survive (the game starts with him nearly getting killed, and subsequently being busted out of a prison transport). Only at the very end does a revenge motive appear.
The most clear-cut Villain Protagonist of the series is Tommy Vercetti from Grand Theft Auto: Vice City. Tommy is not above dealing drugs, and unlike most of the other protagonists, is actually trying to be a kingpin of the trade. The game's plot mostly revolves around Tommy seizing control of Vice City from the criminals who previously controlled it. Also unlike otherprotagonists in the series, he shows little to no remorse for any of his crimes and is only committing them to benefit himself as opposed to protecting those he cares about.
By Grand Theft Auto: San Andreas the first Anti-Hero protagonist appeared, Carl Johnson. In cutscenes CJ is present as an honourable, even admirable character, and his motivation for most of the game is simple survival as well as keeping his family safe. Notably, CJ is opposed to dealing drugs of any nature, the only protagonist in the series that does so. Outside of the cutscenes he's just as willing to murder, steal, and destroy as any of the other protagonists.
Downplayed in the 3 Grand Theft Auto IV stories. The 3 protagonists are more of Anti-Heroes and Anti-Villains than outright villains. Despite Niko, Johnny and Luis committing crimes and doing horrible things, they're quite sympathetic and have rather good qualities. They are shown to care a lot for their friends and families, can help strangers from time to time, and unlike the normal GTA protagonist, their motivations aren't power and greed. Also, when they are killing, in the story missions at least, it's usually other criminals or corrupt people.
Franklin's just a young street hustler trying to better himself (though he doesn't think about going straight either) who's also fairly amicable, but at the expense of often being a doormat other people walk all over.
Michael too is fairly cool and collected though at his worst, he's not any better than his psychotic former best friend Trevor. His impulsive decision making has him return to a life of crime early on in the game much to the chagrin of his family whom he honestly doesn't care all that much for. Near the end however, fortune begins to shine favorably on Michael.
Trevor however, is an almost completely straight example of this, though even he has his moments of compassion. His intro mission alone has him wipe out the Sandy Shores chapter of the Lost MC just to show how unhinged he is most of the time.
Warcraft III has a linear storyline that puts the player in control of different commanders from different sides of the war depending on the point of time in the story. The human campaign features Prince Arthas, an idealistic young man fighting a horrific undead army. As the war carries on, Arthas must resort to increasingly reprehensible tactics, starting with the slaughter of a sleeping town when he learns they've received shipments of food from a village secretly contaminated by the undead plague. Out of desperation to save the human population, he acquires, at the cost of his soul, a magic sword powerful enough to defeat his undead nemesis. The player is still in control of Arthas during the next campaign, but now he's a soulless Death Knight leading the undead in their war against the living.
StarCraft has one campaign for each of the three factions, all of which form a cohesive story. During the Zerg campaign, you're an evil giant brain-slug monster, commanding your evil Big Creepy-Crawlies into killing the good(ish) guys. Likewise in Brood War, the Terran Campaign has you play as the UED, who are pretty bad, although they rarely fight any good guys.
In StarCraft 2 there are four campaigns: Wings of Liberty, Heart of the Swarm, Legacy of the Void, and Nova Covert Ops. While the other three campaigns show their light on the protagonists noble goals, the Heart of the Swarm campaign has several morally questionable moments. These include absolutely destroying the Dominion forces on Char, and wiping out Protoss colonists before they can get reinforcements to save their people from Kerrigan (the player character). In both instances, Kerrigan's behavior isn't waved as acceptable, but rather the result of a brutal revenge plot against Arcturus Mengsk, and casualties occur along the way. Most of these instances try to keep her violence strictly focused towards other Zerg or Dominion forces, but these two examples in particular are incredibly brutal towards innocent bystanders in Kerrigan's way.
In particular, the colonists did nothing to actually deserve their fate outside of defending themselves from an incoming Zerg attack. The captured protoss angrily tells Kerrigan she's murdering colonists, and when they try to flee, Kerrigan sends the protoss, now host to a queen, to their ship which results in the entire ship being effectively devoured.
In Star Trek: Armada, the second to last campaign is the Borg campaign. In the final mission, you successfully assimilate Earth, killing Worf in the process. This is undone via Time Travel in the subsequent hidden campaign, in which the Federation, Klingons, and Romulans join forces to defeat the Borg.
Kratos from the God of War Series is a berserker whose primary motivation is revenge on anyone who has spurned him. Which eventually expands to everyone who crosses his path or tries to stop him doing whatever he's doing. Also a fair few people whose deaths would be convenient for him.
To explain, there are two story paths in the game. The first path, the default, is played by simply not attacking Lady Layna on a new game plus, however attacking Lady Layna will result in her dying and the entire village setting out to kill Revya. Nobody can stop you, and with Gig's power you do horrendous things. Force a man to fight an innocent warrior to save his son, kill a kid out of boredom, subjugate cities and destroy them outright, and generally destroy the land with absolute disregard for anything except entertainment.
The Brotherhood of Nod in general, and Kane in particular, of the Command & Conquer series, especially in Tiberium Wars where a large part of the Brotherhood's basic motivation stems from economic woes, health problems, and perceived oppression and marginalization by the Global Defense Initiative.
Taken up to eleven in Kane's Wrath, where you learn that a previous mission you played in Wars, where you were defending as the bad-guy Nod and were attacked by a rogue group of Nod traitors supposedly led by Killian, where you learn the truth of the treachery. However the perpetrator did it in belief that she would be helping Nod rid themselves of an unbeliever, but unintentionally (however it was planned by Kane) triggering the arrival of the Scrin. What makes this a villain protagonist is that you are now in command of the traitor army. It's hard to understand exactly who she ended up helping in the end, but she's definitely a villain to all factions.
Tie Fighter. You play on the side of The Empire, and have Darth Vader as your wingman. Note that while you do spend quite a bit of time fighting the Rebels, the Empire is portrayed as quite a bit less ruthlessly evil than in the films and other media while the Rebellion is much more violent and perfectly willing to target civilians. The result is more like an Anti-Villain Protagonist.
The Force Unleashed features Starkiller, a Dark Jedi who was raised by Darth Vader and has a disturbing talent for killing his enemies in outlandish, yet surprisingly amusing ways. Justified to an extent as he was raised from childhood to believe in Vader's cause and eventually turns against him anyway (canonically). The non-canon add-on missions included in Ultimate Sith Edition take it further, complete with Starkiller informing a captain "You Have Failed Me For The Last Time."
Star Wars: Battlefront II's Campaign mode. You play as the Republic's 501st Legion, who quite obviously become the bad guys just before the halfway point.
Saints Row 2 has the player becoming this, with the goal of the game being 'take over the city over the corpses of rival gangs, cops and any innocent civilians that get in the way'. The only reason the Saints look sympathetic is via the even worse antics of their enemies and the Undying Loyalty the Saints develop to each other. This continues into the next game, though much more downplayed in favour of chaos and stunts than outright villainy.
It really isn't until Saints Row 4 that the boss is actually forced to admit to or understand the significance of his/her actions, however their amoral and self-righteous attitude never vanishes, it's just given context.
In No More Heroes, Travis Touchdown creates the line in the sand for a character who either just barely counts as a Villain Protagonist (he has very few, if any, likable qualities, and kills people for a living) or is not quite evil enough to be a Villain Protagonist (the people he kills are, for the most part, even moresick and twisted than he is, or at the very least other assassins). Which side he is actually on is up for debate. He still doesn't veer completely away from this in the sequel, in the end murder is the only answer in order to seek revenge and to escape the rankings.
Servant Avenger from Fate/hollow ataraxia is definitely a Villain Protagonist - he is supposed to Evil Incarnate, after all. His soul itself is twisted and Always Chaotic Evil, and he actively pursues murder and rape to pass the time. This does not prevent him from becoming a character you can sympathise with, especially after the flashback to his horrific Start of Darkness and some very poignant conversations with other characters. Despite hating humanity, he still shoulders the responsibility that was forced onto him - to bear every sin ever committed and will be committed by a human and forever serve as a twisted 'champion' of humanity. The ending is complete with a Tear JerkingHeroic Sacrifice.
"Even if humanity is worthless, the history that has been laid down until now has meaning. (...) It is not a sin to exist."
Firebrand of Demon's Crest is, for starters, a Red Arremer from Ghouls 'n Ghosts (the original Demonic Spider). The game starts with him as a prisoner of the demon Phalanax, who interrupted his attempt to take over the world and stole the Crests he was using to do so. Once he breaks out, the rest of the game concerns him reclaiming his stolen property and kill Phanalax so that he can Take Over the World as previously planned.
There are four endings to Silent Hill Downpour which determine if Murphy Pendleton was a villain or a wronged man. There are two good endings, two bad endings, and two secret endings (one which is a joke ending). The worst possible bad ending explains that Murphy both killed his own son, killed a police officer, and killed Patrick Napier. He shows no remorse for it.
Umineko: When They Cry loves to play with this trope, at least in-universe. Namely, in the 5th Arc, Battler become the Endless Sorcerer while a Mary Sue of Bernkastel's creation takes up the 'protagonist' role. (That is, has a reliable perspective.) In reality, though, no face heels or heel faces occur. The 'protagonist' role simply gets taken over by the two most evil characters in the series while they force the good guys into the 'antagonist' role.
In the Rampage games you score points by destroying as much property as possible and eating people, and most of the people haven't done anything to you or are just soldiers doing their job. You can also kick them to death or knock them off building/tear off parachutes and watch them splat.
The Elder Scrolls IV: Oblivion has the Dark Brotherhood quest line, in which the player takes the role of an assassin. It mixes in clearly deserving targets (The very first one is lightly implied to be either a rapist or a murderer) with somewhat-deserving ones (A pirate, who's clearly killed people 'on the job' before) with clearly innocent people. You also get to kill your entire 'family' of assassins, which may or may not qualify for the Moral Event Horizon. Several of the Daedric quests in the game are also pretty villainous, ranging from gleeful sociopathy to diabolic evil: In Molag Bal's Daedric quest, the player is asked to goad a Reluctant Warrior into murder. Obviously, being a sandbox game it also features Video Game Cruelty Potential aplenty.
Dungeon Keeper: Build your sprawling dungeon, employ creatures of darkness, spread your dark influence over the land. Don't forget to deal with those adventuring heroes who want to slay your army and steal your treasure. If the imps or the traps don't kill them, have them tortured.
Caleb, the main character in the Blood series, is a psychotic undead cowboy killing his way through his former cult so he can get revenge on their god, Tchernobog. What pushes Caleb into true villainy is just how much he loves his Roaring Rampage of Revenge; when he isn't wisecracking or snarking, he's cackling like a madman while chucking dynamite at anything that gets in his way. And then, in the second game, his disuse of Tchernobog's powers begins to unravel the very stability of the universe; he's quite happy to let the totality of existence collapse out of boredom.
In the flash game Armed With Wings, you play as the exiled king Vandheer Lorde, the main villain of the series, who is undeniably badass.
Devil May Cry 3: Special Edition adds the ability to play through the story as Dante's Evil Twin, Vergil. However, this is solely a gameplay feature as aside from a new intro cutscene Vergil doesn't have a special story mode and simply goes through Dante's missions as usual, with the only difference being that the Vergil boss battles have a Palette Swap.
Centipede: The comic book adaptation has the playable character (a wizard) in the role of the bad guy, with a boy trying to stop him.
Sands of Destruction has us follow the adventures of the World Destruction Committee. Although only one is actively seeking the destruction of the world, the other is tagging along because he likes our crazed lady protagonist, and the third is going with to protect him.
Okage's main character is a slave of the evil king Stan, and through the game, you're trying to take the power of the other evil kings that showed up while Stan was in a jar, so he can take over the world. It's not very prominent though, what with Stan being a Harmless Villain who spends more time fighting evil than causing it.
The title character in Legacy of Kain is quite the nasty piece of work. The series starts with him becoming a vampire so he can avenge his death. He then decides to destroy the town he was murdered in. And then he gets a list of people to kill, and just settles for slaughtering every man, woman, and child he sees. And right as he's finished, he ruins the whole point of the quest and just decides to rule over Nosgoth's dying remains. In Blood Omen 2, he mind controls bystanders to their deaths, kills every human he sees, and murders his Love Interest when she realizes what a monster he is, all in the name of regaining his empire. It takes Nosgoth itself dying in the Soul Reaver series for him to simmer down, and then, he's a Manipulative Bastard to his vampire offspring Raziel, and is only out to save himself.
Scott Shelby in Heavy Rain especially when it is revealed that he is the Origami Killer masquerading as a private investigator.
This happens in BlazBlue when you play as Hazama in story mode, he's the story's Villain Protagonist, with no past or reasons to justify his villainy. Also the same goes to Relius Clover.
Wizardry IV is an atypical entry in the series: it has the player take control of Werdna, the Evil Sorcerer of the first episode, now resurrected and thirsty for revenge... If he manages to just leave the dungeon where he was buried first, which is not an easy task.
PAYDAY The Heist has you as a crook taking part in various heists, complete with taking hostages and shooting a whole lot of cops.
Jinkuro, the malevolent ghost possessing Momohime's body, in Muramasa: The Demon Blade. He's outright only into the whole ordeal to get his chosen weapon back and find a better target in his Grand Theft Me scheme to live forever, and does a lot of villainous actions (such as invading Heaven) in order to find alternate routes to immortality.
The Voinian campaign in Escape Velocity: Override is about as unambiguously evil as they come. The Voinians are a race of vicious alien warlords bent on conquering the galaxy and enslaving everything in their path. The player has the option to help the Voinians break their stalemate with the human United Earthnote Word of God is it fails and the stalemate ends up broken in favour of the UE, and crippling the attempts of a previously conquered race to rebel against their overlords. Rewards for doing so include access to a variety of powerful Voinian military vessels and the unsettling satisfaction of committing genocide against your own race.
AllEscape Velocity games have at least one storyline where the player character can be called a villain: in Classic, working for the Confederation and trying to bring the Rebels back to heel, in Override, the Voinian and the two Renegade storylines, and in Nova, the Federation storyline (after a certain point of no return).
Brice, a UFO-obsessed ghost and one of the playable characters in the adventure game, Amber Journeys Beyond. After you complete his level he is sent to Hell in a particularly horrifying way - granted, he did murder at least 3 people in the game's backstory.
In Disciples2, the Elves are initially on the side of the "good" guys. In Rise of the Elves, their god Gallean, driven mad by his resurrection and the Trauma Conga Line inflicted upon him by the vengeful Mortis, commands them to be brutal warmongers. Gallean is sick of the Elves always getting shafted by their so-called allies and has them taking what he believes is rightfully theirs by force. The "Villain" part is established in the first scenario, where the goal is to slaughter a town of innocent humans. A few Elves question these orders, but their doubts don't last. Ironically, the only Elf who continues to have reservations about this is the Oracle who relays Gallean's will to his people.
In DEFCON, each player takes up the role of a General Ripper during a global thermonuclear war. Each player's goal is to ensure that the capitalist/communists/whatever die in a nuclear fire. The "Genocide" mode elevates this - the only way to gain points is to nuke population centers.
The Lord of the Rings Online has a monster-play feature which lets you be an orc, goblin, warg, or other baddie minion, and play in a PvP dungeon against hero players.
A staple in Heroes of Might and Magic, due to aversion of No Canon for the Wicked. Examples would be Xeron in 3 and Tawni in 4. Heck, even Tawni's most loyal subordinate who is her real father calls her out for her genocide of the Merfolks!. And she's not even the worst of them all. In the Heroes Chronicles campaigns, the main character Tarnum is this for roughly half of the first campaign (the following campaigns are spent as The Atoner) — he starts out merely ruthless in trying to liberate his people, but eventually goes way too far with it and becomes a brutal oppressor in his own right.
No. 47 in the Hitman series. Granted, he is for the most part killing people much nastier than himself (arms dealers, terrorists, mobsters etc.) and might even qualify as a Hitman with a Heart depending on one's interpretation, but that doesn't really dull the force of playing as a Professional Killer who's not above utilizing some pretty unpleasant methods to get the job done.
This can happen in any Fighting Game that has the villains as playable characters.
The entire point of Deception. Taking over a mansion/castle just to lure adventurers or heroes to messy deaths within does not leave wiggle room for heroics. The character has the opportunity to pull a Heel–Face Turn at the end, but it's by no means obligatory.
Tekken always ends up becoming this. The whole story is centered around the Mishima bloodline, and the conflict between it's generations within it. As one protagonist takes down another antagonist, they end up becoming more of a jerkass than the previous antagonist in the next game, where as the previous antagonist then tries take them down for being worse than they were before. It can get confusing.
Tekken 1 had Kazuya being presented as a Ryu expy hero, with his father Heihachi as the Big Bad and owner of the powerful and oppressive Mishima Zaibatsu Corporation, who Kazuya wanted to take down.
Tekken 2 switched it around. Kazuya took over Heihachi's empire, and became even worse than he was (doning a rather pimp purple suit, and using the Zaibatsu for far more chaotic and malicious things where as Heihachi just used it for order). Ironically leading to Heihachi becoming a sort of Anti-Hero, to take Kazuya down, and the previous villain actually doing the world a good service when taking his company back and restoring the world to controlled peace (although he was obviously only doing it to regain power).
Tekken 3 led to Kazuya's son, Jin, arising as a new Mishima, far more honourable and nicer than any of his family, and for seemly the first time, we believed that he would finally become a moral compass for the family.
Tekken 4 dealt with a three way clash between all three. Jin, former protagonist, hiding in the shadows after the previous game, emerged as somewhat of a Wildcard. While still rebelling against his family roots because of their evil, he started to become too confused, single minded, and spurred on by hate and anger, to really be seen as noble and righteous as he once was. Kazuya and Heihachi were jerkasses, but they weren't even trying to hide it. But the story, at least until the climax, generally focuses on Kazuya wanting revenge, and is somewhat shown from his perspective.
And now with the climax of Tekken 5 leading to Tekken 6, Jin has followed in his father's footsteps and took over the Zaibatsu for himself, and the once believed more heroic than the rest of his family, has become even MORE of a menace than either Kazuya or Heihachi ever have, plunging the entire globe into world war so that chaos is all there is. Thus far, Lars is the only Mishima inroduced, that hasn't become destructive and malicious yet, but only time will tell.
In Quest Fantasy, S O U L tries to portray HERO as one. It's open to interpretation whether he really is, though. Later on, however, played more straight with Guy, who is subjected to the same 'you killed this innocent man' guilt trips the other protagonists are subject to and doesn't even care. He would grow up to become The Dragon.
All three main characters of the Mental Series are effectively this. They rack up a massive body count over all five games, with them killing anyone in their way in order to escape. Fred in The Journey even sets a building on fire and crosses a gap by jumping off one of the inhabitants as they try to leap to safety! All the killings become a plot point in the fifth and final game, Murder Most Foul, where the amount of bodies racked up by the trio makes them the most wanted criminals in the country. Oops.
Despite the title, subverted in Bully, in which the protagonist is an Anti-Hero.
Possible in Baldur's Gate, depending on which alignment the player chooses.
Ellen and the Cocoon organization from Pale Blue are made as villains by the developers in order to provide a perspective flip to the usual heroism tales such as Power Rangers, Kamenrider and Ultraman.
Assassin's Creed: Rogue has you playing as Assassin turned Templar Shay Cormac as he participates in the purge of the Colonial Assassins.
Bass from the Mega Man (Classic) skirts the line between this and Anti-Hero whenever he's playable. He never stops working for Dr. Wily and trying to kill Mega Man, but his desire to prove himself as the world's strongest robot can cause him to save the day by accident. His sole reason for turning on Wily in the Power Battles games is to get him to acknowledge that he's his greatest creation and that he doesn't need to create other Robot Masters to take down Mega Man, and when King declares himself king of the robots in Mega Man & Bass, Bass goes after him to prove that he's more worthy of the title instead.
An interesting variation in the Walking Dead series: Tavia, the final playable protagonist of DLC 400 Days, who wasn't revealed to be working for Carver, Season 2's Big Bad until Episode 3 of the next season.
Guilty Gear XX Accent Core+ feature's Justice's Story Mode, which is a reenactment of the events of the first game, and has the player use the first game's Big Bad to beat the crap out of the original roster and kill Kliff before Sol finally comes in and puts a stop to things.
At least in the first game. The sequels make him more of a Nominal Hero.
Wario Land Shake-It could possibly tread carefully between being this and just coming short. Wario is in it for the money but he is also saving a lot of people. That said, after he saves the queen he simply tosses her aside and robs her of her bag of riches and ditches the universe. One could say he earned it for saving all of their lives, but he was a serious jerk about it and simply up and tossed the queen like a bag of garbage.
In Custer's Revenge, you play as commander George Armstrong Custer as he tries to rape a native American woman.
In Jaws Unleashed, you play as the titular shark, eating people and causing mayhem.
The protagonists from Kane and Lynch are an interesting example. Since they are the POV characters, we find out a lot about them. They both have traits that make them sympathetic. Kane is motivated by love for his daughter, Lynch struggles with severe mental illness and most of the time they are merely looking for a way to survive. However, they WILL kill anyone between them and their goals. In any other work, they would be co-Brutes and get killed by The Hero about an hour in.
The majority of playable characters in both Hotline Miami and its sequel either fill this role or sit on the far end of the Sliding Scale Of Anti Heroes. First there's Biker from the first game, who's trying to get out of the professional killer business not because of any moral quandaries, but simply because he's bored. The second game adds in Jake, a racist neo-confederate working for 50 Blessings, the Fans, a gang of thrill-seeking copycat vigilantes continuing Jacket's work from the first game, The Son, the new leader of the Mafiya trying to take back his turf from invading Columbians, and Manny Pardo, a Cowboy Cop who uses his position as an excuse to go on killing sprees and is the very same Serial Killer he's supposedly been hunting for the entire game. Martin Brown is a maybe-example, since everything he does as the Pig Butcher is part of a movie, though he admits in a dream that he's an utter psychopath who relishes in being able to act out his violent fantasies on camera. Evan also can be viewed as maybe-example, since while he appears to be a person who tends to avoid violence (at least using lethal methods, unless player enters his so-called Rage mode, by killing few downed enemies) and aint homicidal maniac, criminal or lunatic unlike majority of other protagonists, he is obsessed with his book to the point that he even storms the whole club that belonges to Russian Mafia (even though unintentionally, but even in rage killing a guard who refused to let him in) and beats/kills everyone there just to ask one of them some information and depending on player's choice he can also chose to continue writing his own book over his own family. Even Jacket himself could count, though it's offset by his obvious Sanity Slippage and a girl he rescues from the Mafiya that becomes his Morality Pet.
In Undertale, killing every monster in the game causes the protagonist to develop a genocidal personality, going so far as to lose their humanity and become a heartless killer.
Torque from The Suffering series can be example of such trope. Depending on player's choices he can either help people in need, ignore them or kill them himself. Player's actions also depend on the endings of the games and thus is he responsible for the death of his own family or not.
Juan (later Jesus), protagonist of the game 12 Is Better Than 6 is a Mexican outlaw and alcoholic, who cares only about himself and will kill anyone who stands on his way, oftenly acting really arrogant and rude towards others to the point that he can even hurt or kill them (even though oftenly he is provoked in such situations), later in the game it's also revealed, that he used to be the leader of the violent Mexican gang before they betrayed him. Also, it's implied that he hates white people, at least Americans, thus also making him racist. However, he does show some decent qualities, like feeling bad about his past and wanting to warn a barber in one town about upcoming outlaw attack.
Henry from the Henry Stickmin Series is a light-hearted example who's also a massive Butt Monkey prone to The Many Deaths of You. He does work with the government to take down a criminal organization in Infiltrating the Airship, but can choose to instead become the criminal organization's new leader or abscond with a jewel stolen from the airship's vault.
Ayano Aishi, AKA Yandere-chan, the player character of Yandere Simulator, who will do anything to get her Senpai. This includes slandering, kidnapping, torturing and murdering her rivals, and she has zero qualms about any of it.
Word of God: Remember, Yandere-chan is not a nice person. She is a monster.
Reviel Von De Russert from Nocturne (RPG Maker) is a vampire ancestor who has a history of mass-murdering humans under the rationale that their mortality makes them about as worthless as a Random Encounter. Though he does a Heel–Face Turn when he realizes that he grew to care about a village that he originally planned on destroying.
The Addams Family: The game for the Turbo-Grafx 16 based on the 1991 movie has you in control of the dead-beat Amoral Attorney Tully Alford who schemes to steal the Addams family fortune and in the game fights the family who see it as a fun treasure hunting game. All the videogames based on the movies qualify to an extent considering that Gomez and Fester in "Addams Family Values" are villainous and proud about it, though the games have them more trying to save their family than feeding people to their pets.
A LOT of videogames that come from "Looney Tunes" have you in control of a predator or hunter who tries to catch and kill his prey very much like the cartoons themselves. That is when they aren't in the role of Nominal Hero which they are just as often. A few examples: games based on "Sylvester the Cat and Tweety Bird" like "Breakfast on the Run" and "Cagey Capers" have you in control of Sylvester the Cat and trying to make a meal out of Tweety. "Desert Demolition" starring "Wile E Coyote And The Roadrunner" is a partial example as you can choose if you will control trapper and predator Wile E. Coyote or prey Roadrunner. In the "Looney Tunes Collector Martian Alert" sequel "Martian's Revenge" Marvin is they playable character and wishes to turn Daffy into a roast duck for making fun of his previous game's attempts to blow up Earth.
The title character in Bob's Big Adventure is a minotaur. As it's Played for Laughs a fair bit, this leads to enemies like the "Inexperienced Adventurer" and "Novice Mage."
The "Darkspawn Chronicles" DLC for Dragon Age: Origins lets the player control one of the Darkspawn commanders in the Battle of Denerim, in an Alternate Timeline where the player-created Grey Warden perished at Ostagar, leaving just Alistair to shoulder the Order's duties.
In the Wacky RacesLicensed Game for the NES, the player controls Muttley, and the goal of the game is to rescue Dick Dastardly. The Wacky Racers serve as the game's bosses.
The Batter in OFF. In short, his operational definition of "purify" is "destroy". This includes what he's trying to do to the world. Returning to any zone after it's purified will provide a fairly strong hint to this, but the battle in Zone 3 with the Critic-Burnt - who barely even looks Burnt and does nothing but cry for help - is the point at which most players realize they're playing as the bad guy.
Considering that D-Class units are often convicted inmates on death row, it was greatly implied that the protagonist of SCP - Containment Breach is one of these, before one of the SC Ps (SCP-1074) that he took multiple people's lives and has a Villainous Breakdown over it.
In the 1982 video game adaptation of The Texas Chain Saw Massacre, you play as Leatherface, and the goal is to murder women with your chainsaw. It is one of the earliest examples of this trope in video games, and at the time of its release, it caused considerable controversy.
In Super Columbine Massacre RPG!, you play as Eric Harris and Dylan Klebold planning the massacre, setting up the equipment needed, arriving at the school unnoticed, planting the bombs at the cafeteria, raining bullets on unfortunate students and faculty, and ending their own lives when the police exchanged fire with them.
In Bank Heist for the Atari 2600, you go around robbing banks and blowing up cop cars with dynamite.
In Calm Time, you play as a guy who has invited a bunch of people over to murder them, among them, a child. He had already killed a woman he trapped in his basement.
The Web GameZombidle is an Idle Game about the kingdom of Goodlandia versus Bob the Necromancer and his army of zombie minions. You play as Bob and his minions, and most of the "enemies" you destroy are the houses and buildings of innocent people (and the burning people that escape once the houses are destroyed), with the occasional line of doomed guardsmen as a boss battle.
In Varicella, you play as a scheming minister who plots to kill off or otherwise incapacitate all of his rivals to become the regent to the throne. This is made somewhat more palatable by all your rivals being even more awful human beings than you.