A renegade Shepard's actions can be explained by this through the Colonist or Earthborn backstory option.
Jack was raised as a test subject and was encouraged to be violent and wasn't allowed normal relationships. She seems surprisingly well-adjusted, considering.
Miranda begins 2 as an Ice Queen extraordinaire. It's shown that before meeting Shepard only three people to her knowledge never betrayed her trust. Her father is an absolutely despicable human being who grew her and her older sisters in test tubes, only to kill all her older sisters for not being worthy of preserving his legacy, viewing her as nothing more than his "perfect" property to satisfy his galaxy-wide ego. Her rescue of her baby sister and escape from her father had her join a xenophobic terrorist group, Cerberus, for protection. Her "perfection" has ironically resulted in a major inferiority complex that makes her incapable of crediting herself with her own successes. With Shepard's help she can get over this, and ends up being one of the warmest and kindest people in the series.
Defied by Kaidan. Of all the series' human squadmates, he has the most justifiable reason to have issues with Fantastic Racism against aliens in general and turians in particular. If the player chooses to suggest that this is the case, Kaidan is not amused and pointedly refuses to use his past like that on the grounds that it would make him a hypocrite.
Downplayed with Kefka, who's insane because the process that made him a Magitek Knight shattered his sanity.
Sephiroth from Final Fantasy VII was raised by his father, the evil mad scientist Hojo, who regarded him as little more than a human lab rat, and was trying to turn him in to the perfect super soldier. Obviously, Hojo mostly succeeded. Being told his mother died giving birth to him and then finding out that his "mother" is a monster couldn't have helped, either.
Everything regarding Anti-Hero Squall's screwed-up mental state in Final Fantasy VIII can be traced back to separation issues at a very young age when Ellone was taken away from him at the orphanage. Compounded by an apparent complete lack of emotional support following their separation, and by the fact that junctioning Guardian Forces during his training caused him to forget his childhood, making it impossible for him to re-evaluate his childhood trauma from a more mature perspective.
Ultimecia's whole motivation behind her evil is being feared and hated for something she hasn't even done and doesn't know she's going to do yet.
According to Takashi Tokita, this was originally written down in the script, but 3/4 of the script were removed in the Super Famicom version, and it wasn't until they made the DS remake that they could implement it in. In other words, the DS remake was actually more of a directors cut.
Shadow The Hedgehog has one as the main purpose for his motivation in Sonic Adventure 2, due to the death (metaphorically) of Maria Robotnik, he vowed vengeance against all of humanity He remembers later that Maria does not want that, and wanted him to forgive humanity for there are some good people in the world.
And in his spinoff game, we have the GUN Commander's motivation for his seemingly blind vendetta against Shadow. It turns out that he was one of the (very few) survivors of the Ark Disaster, and, like Shadow, was a close friend of Maria. The Commander's hatred for Shadow was because he blamed him for Maria's death, believing that if Shadow had never been "born", Ark wouldn't have been wiped out and Maria wouldn't have died. He realizes the folly of this reasoning in the True Ending, however.
A great majority of villains in Sly Cooper games have one of these. Let's see...
Muggshot was picked on as a child, so he wanted to be a gangster.
Mz. Ruby had no friends as a child, so she learned to summon the dead in order to have some.
Panda King spent a decade mastering fireworks, but the rich noble men turned him down because of his poor background.
Dimitri had been rejected from the art community (it wasn't that good to begin with).
Rajan was born into poverty on the streets of India.
The Contessa lost her husband. However, we are meant to believe she killed him herself.
Jean Bison was frozen during a mining accident.
Arpeggio never grew from his minute size, so he couldn't keep up physically with his peers and couldn't fly.
Octavio's chances at opera were ruined when Italy began to favor Rock 'n' Roll.
Dr. M leads us to believe he was mistreated by Sly's father when they were working together.
The Grizz lost his wealth and fame fast after briefly becoming a graffiti artist.
Ms. Decibel had a failed career as a musician and her trumpet stuff inside her trunk.
One was given to the recurring villain of Final Fantasy X, Seymour Guado. In a nutshell, Non-human dad marries human mom, but his species' xenophobic civilization doesn't like that their leader married a human, so she and Seymour are exiled to a long-abandoned temple. Mom decides that Seymour will need to be powerful to be accepted, so she undergoes a procedure that will allow him to call on her as a powerful summon beast but will also turn her into a statue while young Seymour is crying for her not to, effectively meaning he's been abandoned by both parents. Summon Beast Mommy looks like this. Even worse is that after this Seymour was expected to use said beast to destroy the monster Sin, which would make him famous throughout the land... and also kill him.
For all the evil that he did afterwards, Ganondorf from The Legend of Zelda series had a fairly understandable reason for his desire to conquer Hyrule and claim the Triforce: His people were trapped in a lifeless desert, forced to steal from others just to eke out a life. Seeing his people in such despair, and then seeing a land in spitting distance that was rich, prosperous, and inhabited by people who didn't even realize their good fortune, made Ganondorf understandably VERY angry. Supplemental material like the official Nintendo Comics, and brief mentions in The Legend of Zelda: Ocarina of Time, hint that Ganondorf actually tried to invade Hyrule the old-fashioned way. When that fails and he is forced to swear fealty to the Hyrulian king, he turns to searching for the Triforce as a second option.
It gets even worse in Skyward Sword, where it heavily implies that the reason behind Ganondorf's evil is because he's the reincarnation of Demise's hate, meaning he's been screwed up since before he was born to do evil.
Not only that, but it's also revealed that the desert the Gerudo would eventually come to inhabit wasn't always like that - no, it was once as lush and fertile as Hyrule is in other games, not to mention even more technologically advanced, but was sadly stripped of its resources and left to wither away and die by an ancient civilization.
Zephiel was a kind and loving boy in Fire Emblem 7, but his father Desmond hated him. This hatred, ultimately resulting in Desmond attempting to kill Zephiel, was the only reason why Zephiel turned out to be a misanthropic tyrant in Fire Emblem 6.
First Encounter Assault Recon's entire storyline is one giant Freudian Excuse in which the main villain, Paxton Fettel, sets out to free his mother, Alma, who was a powerful psychic who was used as a living incubator for psychic supersoldiers since she was eight years old, and had her children stolen from her in front of her eyes. Incidentally, the project lead who was behind this whole round of depravity turns out to be Alma's own father, Harlan Wade.
Prince Luca Blight from Suikoden II is one of the nastiest, evilest, and most badass villains ever conceived. He makes some pretty good attempts at subverting Infant Immortality, even. He also kills a unit of his own country's soldiers (The 'Youth Brigade', even - kinda' like heavily armed boyscouts), kills his father, usurps the throne, starts a war, and unleashes some Sealed Evil in a Can to depopulate a large city completely. However... When he was 6, he watched his mother being raped by soldiers from the country he's invading in the present, while his father ran to hide in the capital. The kidnap-rape wasn't just a random act of malice by enemy soldiers, it was ordered done by the then mayor of Muse. Even though the Highlands and Jowston were indeed at war, they weren't invading anything, they were non-combatants. Luca's mother died nine months later, which was when his little sister was born. The little sister, who grew up to strongly resemble her mother and thus serve as a living reminder of the horror that he'd witnessed all those years ago. He was seeking revenge on both his father, and the country he blames for the events.
Suikoden IV has Graham Cray, who masterminds a war and creates a Weapon of Mass Destruction... motivated by his Start of Darkness: the True Rune of Punishment, which was sealed away on Obel Island, once chose him at its host. To avoid being consumed by the rune, he chopped his own hand off... at which point it jumped to his son. Though he begged his son not to use its powers, the boy naturally ended up disobeying him... using its power to destroy the soldiers raiding their village. Oh, and the soldiers were part of a False Flag Operation being pulled by the Scarlet Moon Empire, Cray's superiors. Naturally, they blamed him for the incident, sending him off in shame to start plotting revenge. So the whole thing's just so he can try and reclaim the rune, reuniting him with some small piece of his son.
In Suikoden V, Gizel Godwin and Euram Barows share a Freudian Excuse, in a way: both of them had loved ones killed by Nether Gate, the Queendom's cabal of assassins, during the bloody Succession War. For Gizel, it was his mother; for Euram, his elder brother, who was supposed to be his father's heir, thrusting him into a role he hadn't expected. They cope with this trauma in different ways, neither of them really all that good.
In Star Control II, the Ur-Quan reveal that their entire race has a Freudian Excuse: They were psychically enslaved until they discovered that their masters could not command beings that were in excruciating pain. After earning their freedom they vowed to protect themselves from ever suffering such a fate again. This in combination that the fact that the green Ur-Quan, who enslave other races, are relatively benevolent when their orders are obeyed, makes them more of an Anti-Villain. The Big Bad black Ur-Quan, on the other hand, just want to kill everyone.
Word of God has it that the Ur-Quan were in fact based upon real-life acquaintances of the creators who were abused as children and the effects it had on them.
Sam: Why do you persecute harmless bigfoots? Conroy: Harmless? Harmless? I'll have you know my parents were killed by a rabid bigfoot! Sam: Really? Conroy: Well... no. Actually, I'm just a warped evil person who gets his jollies torturing innocent woodland creatures. Sam: Well, that's a valid motivation too.
On the other hand, some of them are handled well enough that they actually make sense-Sasha's obsession with keeping one's mind under control stems from the incident that prompted him to leave home-an amateurish psychic foray into his father's mind to learn more about his dead mother ended up dredging up some contexts he wasn't quite ready to see his mother in. Like the context that culminated in Sasha. And Milla is haunted by the deaths of the children she used to be a nanny to, but she doesn't let it get in the way of things. And then there's Ed Teglee's, which even he admits is a little pathetic, once he gets over it.
The final boss is Raz's and Oleander's Freudian Excuses combined, essentially a grotesque combination of their fathers.
Further subverted in that Raz's actual father helps him fight the nightmare. Turns out Raz just needed to communicate with his father more; it was really all one big misunderstanding.
It's a fairly common theme in the Metal Gear series:
A nice example is from the non-canon Ghost Babel, wherein serial-killer-turned-special-agent Marionette Owl reveals the beginning of his gruesome murder spree stemmed from finding the love of his life disemboweled and dismembered, and realizing the beauty of death.
Dr. Koppelthorne in Metal Gear Acid 2 primarily did the stuff he did because he wanted to revive his wife who was killed.
Kojima seemed to be so set on giving Psycho Mantis one of these in MGS1 that he ended up giving him two. In codec discussions early in the game, Mantis is said to have worked for the FBI is a psychic profiler until he dove too deep into the mind of a mass-murderer and took on his personality. When he's defeated in battle, Mantis says his murderous ways are caused by accidentally having killed his father as a child and being forced to witness that all human beings only exist to procreate, with no mention of the FBI.
Big Boss himself had to endure several of his allies being exploited by the government, sometimes just being sold out to their enemy to cover up their secrets, and he had been used to kill his mentor just because they didn't want to abort a mission to steal the legacy from the enemy and yet avoid nuclear war (and that's just going by the abridged version of the true reason for his being recruited to kill The Boss, In the unabridged version, it was deliberately set up that way specifically because they feared her charisma and planned her death from the beginning, and manipulating a sadistic GRU colonel into firing on his own countrymen and create an international controversy just to have the excuse to have her killed.), and his own friends use him for things, even taking his DNA and cloning him without his consent. Finally, he hits his breaking point when his entire home gets destroyed and he falls into a nine year coma, only to wake up to find that the whole world wants him dead! Being reduced to a bitter old man with a vendetta, it's no wonder why he would end up founding Diamond Dogs, Outer Heaven and Zanzibar Land, each a gradually decaying and increasingly warmongering and authoritarian version of his utopic Mother Base for Militaires Sans Frontieres, which was essentially an anarchist commune and one of the few times he has been genuinely happy.
Xenogears; Fei/Id/Grahf and maybe even Ramsus and Krelian.
Bulleta/B.B. Hood in Darkstalkers... maybe. It's implied that she really is Little Red Riding Hood, with all that entails, but this has never actually been outright confirmed or disproven.
In Silent Hill 2, Eddie used his humiliating childhood traumas to excuse his violent methods of coping with the way people look at him. And by "violent", I mean murder.
In Silent Hill 3, Vincent blames Claudia's religious zeal on her father abusing her. This apparently deeply affected Vincent as well, which raises a host of questions about just how early in life he was involved with the Order. Unlike the example from Silent Hill 4 above, however, the player is less likely to be sympathetic towards Claudia, considering what she did to kick the plot off. And then there's the possibility of how she treated the children in the "care" of the Order...even though by the end of the game, she apologetically admits to failing in her mission to turn the world into "Paradise", too. It's not enough by then.
Depending on your interpretation (and which games you consider to be cannon), one possible explanation for LeChuck's evil aggression is his unrequited love for Elaine. However, later games indicate he was evil before meeting Elaine (he IS a pirate, after all). Most recently, the manipulative nature of the Voodoo Lady seems to be a possible source of his evil.
Valkyria Chronicles has Maximilian, who tries to conquer the world because his mom was unpopular amongst the nobility, and then was killed.
The GBA game Nightmare Before Christmas: The Pumpkin King explains that Oogie used to be the leader of the holiday called Bug Day. However, it was forgotten and the town was destroyed, leaving Oogie as the sole survivor. The reason he wants to take over Halloween Town is to re-make it into a new Bug Day. This also explains his dislike of Jack in the movie.
Most of the major villains in Dark Cloud 2 (Dark Chronicle) have one of these; notably Dr. Jaming, Gaspard, and Emperor Griffin himself. The only exceptions are Flotsam and Dark Element.
The good-aligned path in Baldur's Gate II: Throne of Bhaal is to accept that Sarevok, Big Bad of the first game and the protagonist's half-brother, could just as easily have turned out like the protagonist and vice versa had their childhoods been swapped.
This was also a plot point in the first Baldur's Gate, in which his lover asks you to subdue him, rather than kill him (she'll help you only if you agree) for that exact reason. Later, when she tries to fight you in order to protect him, you can decide not to fight her (in what would lead to her slaughter, she knows this). This shakes her out of her delusion and helps her realize that while you are both tied to the same destructive heritage, he has chosen his path, and has no real excuse. She then steps out of the way.
In Dragon Quest VIII, Marcello, manipulative Jerk Ass extraordinaire, is revealed to be the child of an affair between a sleazeball noble and his maid. When the noble's wife gives birth to a son, who happens to be Angelo, the noble ousts both the maid and the young Marcello without a penny to their name, just to cover his tracks. Marcello's mother soon afterward died of sheer despair, leaving Marcello alone to struggle to survive in the world, eventually joining the clergy. However, throughout his time in the clergy, most of the higher ups constantly looked down upon and outright insulted him just because he was of common blood, despite the fact that he quickly became a prominent figure in the church's Templar branch. All of this resulted in what Marcello is in the game proper: A bitter, condescending, overly ambitious prick who blames Angelo for everything he went through, and while this is technically true, he takes his bitterness over it way too far.
In Pokémon Black and White, N is perceived as a well-intentioned extremist since he wants to separate humans and Pokémon because he thinks that humans treat the latter like tools. The reason for this is because his father, Ghetsis, deliberately neglected him so that he would become what he is now. N was raised with abused Pokémon for a good portion of his life and believed that humans were evil (aside from his "subjects" in Team Plasma), setting Ghetsis' plan into motion so that he could make Pokémon illegal for everyone but himself so he could rule Unova. Ghetsis even tells N that he's 'a monster incapable of understanding humans.'
The sequel shows Team Plasma ( At least the ones run by Ghetsis) as being Hugh's Berserk Button. He seems to be laser-focused on making Team Plasma pay. You learn that Team Plasma stole his sister's Pokémon. Who is now following the Shadow Triad.
Cyrus is said to have been under intense pressure as a child to live up to the demands his parents put on him. Despite being so intelligent and such a good student that people in his hometown still talk about him as such when he's in his late 20s, he could never live up to his parents' standards. His plans involve him becoming a god—a perfect being, ruling a perfect world, with perfect people, no matter what that entails.
Silver from Gold/Silver/Crystal and their remakes also has one. He pushes the player character (or anybody for that matter) around, mistreats his Pokemon and most all, detests Team Rocket with a burning passion. A deep-seated psychological excuse is hinted at in the original games, but what it is never comes to light. However, the Celebi event in Heart Gold and Soul Silver reveals that his father is Giovanni, the leader of Team Rocket, who abandoned him after the events of Red/Blue/Green/remakes after being defeated by the hand of Red; not wanting to be weak like his father, he became obsessed with strength and grew a major Inferiority Superiority Complex as a result.
Trevor in Grand Theft Auto V intentionally invokes this trope, and not sarcastically either. It comes as even less convincing here since, compared to Trevor, CJ was practically a saint.
Brucie in Grand Theft Auto IV hates people that are poor but hates fat people even more. He only expresses his dislike once or twice and generally remains as the overbearing testosterone filled friend to Niko. Brucie eventually opens up that when he was a child, he used to be fat and everyone at school made fun of him. Since then, Brucie has become obsessed with exercise and appearance to keep himself fit and shedding the pain he went through when he was overweight.
The Ballad Of Gay Tony reveals that on top of the above, Brucie's older brother Mori is (or at least claims to be) better than "Baby Brucie" in every way (we see Mori beat him at chess, force him to do pushups, and belittle him every chance he gets, among other things), which ferther fuels Brucie's inferiority complex.
Count Bleck, the Big Bad of Super Paper Mario, had a pretty understandable and sympathetic reason for causing the events of the game: He was originally a man named Lord Blumiere, and he fell in love with a woman named Lady Timpani. However, his dad didn't agree to the relationship, and thus exiled her to several dimensions, causing him to kill his dad in grief and summon the void in an attempt to commit suicide. In other words, love made him evil, and it also acted as the very thing that turned him back to good and undo the Void once he found out that Timpani, AKA Tippi was alive.
Napoleon LeRoach, the Big Bad of the second SPY Fox game, was made fun of for being too short for a certain ride at the World's Fair. This led him to come up with the Giant Evil Robot Dog plot, where the giant robot is not only taller than everyone else, but also a ride that activates as soon one million people go through the Fair entrance.
The Elder Scrolls: Oblivion has Bellamont, an assassin who turns on the Dark Brotherhood and tricks you into murdering most of their leaders. According to his diary, he was driven insane after watching Lucien Lachance murder his mother and joined the Brotherhood so he could murder them one by one in revenge. He still keeps his mother's head and apparently has delusions of it speaking to him.
The Shouty Guy from Mondo Medicals apparently (as far as his insane Engrish ramblings can be believed) witnessed his father dying from cancer and this shock was at least partially responsible for his decision to begin curing cancers via killing the patients, including killing the player character under pretense of curing cancer.
In one instance of Fallout: New Vegas, the player can take advantage of this with a high enough Medicine (and thus sufficient knowledge in psychology), telling an angry Supreme Chef that his tendency of yelling at people is him projecting his daddy issues. Upon realizing how shitty his childhood was, he will then run off and cry, leaving his kitchen to you.
In Dragon Age II Meredith's Freudian Excuse for being an extreme Knight Templar is revealed if you are supportive of the Templars throughout the game. Her younger sister was a mage, but Meredith's family hid her so that she wouldn't have to go to the Circle. Her sister lacked the strength and training to resist the demons of the Fade, and she became an abomination that killed the rest of Meredith's family before she was put down by the Templars. As far as Meredith is concerned, any leniency towards Mages could lead to similar tragedies.
Many people online should at least have some awareness of the Allegedly Free GameAdventureQuest, and its prequel DragonFable. Both games are full of puns (we aren't kidding, even the designers and game characters lampshade this) and are generally very comedic in nature, but the way they create their villains are a lot more mature than they let on.
Drakkonan: Used to be a friendly blacksmith apprentice. His entire hometown was burned to the ground by a massive fire dragon, and the main hero of the story (that's you) fails to save his family, which causes him to befriend a less than stable fire mage named Xan. Xan teaches him how to cast fire, and Drakkon becomes one of the most legendary villains in the game's history.
Sepulchure used to be a legendary hero in the DragonFable timeline, but then he lost a "loved one" and apparently began to fall, and fall, and fall...until he goes from being a Fallen Hero to a class-A Big Bad.
Ironically, Sepulchure actually treats his daughter with lots of love as a baby in DragonFable ... speed up to the MMO AdventureQuest Worlds where Gravelyn is not only an adult, but is also evil. She has no Excuse.
Spoofed in the Team Fortress 2 comic "Meet the Director." The Director attempts to pin some of these on the Heavy and the Sniper. They are bemused and unamused, and the Heavy insists on talking about his minigun instead.
The Director: If you could pick one word to describe yourself, Mr. Mundy, what would it be?
The Sniper: Er. Well...
The Director: I'm going to answer that for you. Victim. Of the educational system. Of the role society has shackled you with as an Australian, of course. And let's not forget the current administration, which...
The Sniper: Wait, back up. What'd these folks do to me again?
The Director: Forced you to be a killer.
The Sniper: For the last time, mate, I'm a professional.
The Director: Exactly. A victimized professional killer.
In the 1st Degree has artist James Tobin charged with first-degree murder and grand theft. The interrogation tape of Yvonne Barnes suggests that Tobin ended up doing these things because his wife Helen divorced him. However, she did that because she apparently got fed up with his ways. This would indicate that Tobin may or may not have much of an excuse for what he did.
Shar-Teel, a character who can join your party in Baldur's Gate, is classified as Lawful Evil and she Does Not Like Men. Her biography says that she also hates Flaming Fist mercenaries and that "...likely her childhood was not of storybook quality." This all makes a bit more sense when you meet her father; he's one of the villains in the game, and he's also a corrupt member of the Flaming Fist.
River City Ransom has this for the Big Bad, Slick. Slick was actually Simon, a friend to Alex. He grew jealous that Alex was always better than him in everything and got all the attention, so Simon started the events of the game just to get revenge on Alex.
Speedy Dave who was trying to protect the natural world. It's more left to the viewer's imagination; but it's probably easy to assume the rapid modernization of the world caused him to lose his home or a childhood site he loved to visit.
Princess Pride of Creamland. Creamland was one of the first nations to go online, but was soon ignored by other bigger nations that went online later.
Gauss Magnus was born to a poor family. His brother was adopted by a rich family, but not him. Then his parents became ill and died, leaving Gauss with nobody. So he worked hard to get rich and break the society from within.
The leader, Sean, was orphaned in a plane crash. Despite inheriting a fortune from them, he was forced to live with cruel relatives and was ostracized by society. He also mentions that he was being picked on, too. The internet was the only way he was able to make friends, so he played at being an adult and made net-friends in everyone else, who came together to form Gospel.
The only members who don't have a Freudian Excuse of some kind are Arashi and Dark Miyabi. considering that Dark Miyabi was a Punch Clock Villain and Arashi wasn't...that says a lot.
Solo in Mega Man Star Force was picked on, excluded and attacked for being different as a child, and this combined with his status as the Last of His Kind has left him with a towering hatred of even the idea of friendship, believing that only weak people form groups.
In 3 Jack and Tia were orphaned because their home country was devastated in a war for its technology, so they worked for King to gain access to Meteor-G and destroy all technology.
All the stuffed animals in Die Anstalt are crazy, and part of the puzzle in the game is figuring out why:
Lilo the hippo is withdrawn to the point of autism because he blames himself for one of his former owners getting caught cheating on a math test.
Kroko the crocodile is paranoid and afraid of water because he was abandoned in a public restroom, and used as a mop-head by the cleaning lady, who callously discarded his beloved hot-water bottle.
Dolly the sheep seems to have a canine Split Personality because she's a reversible plush (sheep on the outside, wolf on the inside) who repressed her "other self" after being used as a chew toy by a dog.
Sly the snake is prone to hallucinations because he was used to hide his owner's drug stash, and was abandoned on a highway so they wouldn't get caught; after getting his tail run over by a passing car, his body absorbed some of the hallucinogenic drugs which were stored inside him.
Dub the turtle is obsessed with exercise because he was lost at an airport, and was unable to catch up to his owner because of a moving sidewalk.
Dr. Wood is a psychologist with a few issues of his own that culminate in him succumbing to narcissistic personality disorder and starting a cult. This is because he spent years in a display case in a pediatrician's office, watching children who wanted to play with him but couldn't.
In Story of the Blanks, we see a village where everypony was cursed after they killed a mare who got her cutie mark. Then there came an episode of the show where a disease causes an overabundance of cutie marks, with the likelihood of dying from exhaustion, and that it caused a lot of trouble back in ancient times.
The big bad of Duel Savior Destiny, Downy Reed, is evil because when he was young he and his sister (like many others where he lived) were forced to fight to the death for the amusement of some corrupt noble. When he grew up, he tracked down the noble with the intent of getting revenge, only to find out the man had died peacefully in his sleep surrounded by friends and family. Completely devastated by such an unfair world, he swore to remake it.
Wolf's background in PAYDAY: The Heist explains he is out stealing cash and other valuables because the bad economy made his business sink and his family became homeless.
Mir from Ar tonelico is a source virus that invokes Kill All Humans plot fairly because they were horrible jerks that abused her terribly beforehand. The heroes have to acknowledge her traumatic past before going to fight her, otherwise you get a bad ending.
Most of the villains sport twisted backstories portrayed with varying degrees of sympathy and tragedy, but the games do make it clear that they're insane tyrants beyond redemption.
Dr. Tenenbaum defies this trope explicitly in one of her diary entries. She was a prisoner at Auschwitz, where she discovered science the Nazi way, but says that she saw them as kindred spirits, not tormentors.
Mystery Case Files: Escape from Ravenhearst is one long excuse for Charles Dalimar, who implied that his miserable childhood and commitment to an insane asylum were what made him what he was.
Played with in Haunted Halls 4: Nightmare Dwellers where in the bonus chapter Dr. Blackmore revealed that he was megalomaniacal and twisted even as a child.
Clive Barker's Undying: It is pretty clear that whatever the siblings did at the Standing Stones is responsible for a LOT of their behavior (especially what they did after they died).
In Deadly Premonition, the killer is revealed to be George Woodman. It's also revealed that he had an abuse mother who beat him so bad, she left horrible scars on his back and one on the side of his face that still bleeds when he becomes emotional. During the boss fight after he's seriously injured for the first time, he starts begging for his mother not to beat him. It's also revealed that George was holding his hatred for women deep inside because he was in love with Emily who he believed was special, but starts his killing spree after she rejected him and let himself be manipulated by the game's true big bad.
The title character of Misao has a pretty tragic story. Her whole backstory is revealed whether the player chooses to kill Tohma or Mr. Sohta. Years prior to the story, she was bullied by other kids. Her childhood friend, Kudoh, initially started defending her and even hung out with her. However, he started getting teased and eventually stopped spending time with her. Then, within the last few weeks of her life, she started dating Tohma, which seemed nice at first. She then finds one of her texts on the school board and was targeted by Yoshino and her group. She even saw Tohma with Saotome one day and found out who posted her message. Eventually, Yoshino had a boy sexually assault her in the bathroom and this finally broke her. Later that night, Sohta found her crying in a stall and Misao told him everything. He seemed to be understanding at first, but he then started making advances. Frightened, she let out a Big "NO!", which angered him and he strangled her. It's pretty understandable why Misao would be upset by the people in her life. All, if not most, of them have caused pain in her life and she wanted some retribution for their actions.
Oddly enough, Mr. Sohta has one himself. For as long as he could remember, no one has accepted him for some reason. A majority of his class rejected him for his appearance and deemed him disgusting. Even when he tried to do something nice, there was something that went horribly wrong (such as trying to save a dying cat and returning a handkerchief to a classmate). One day, a girl he had a crush on decided to start hanging out with him. She seemed to be the first person to accept him, but when he confessed to her, she rejected him, claiming her time with him was done out of pity. Because of this, she thought it best to stop meeting with him. This was the last straw for him and he finally broke. He shook her violently while demanding to know why no one accepted him. You can only access this backstory by obtaining the official ending.
The Tales games love making the villains sympathetic. In Tales of Graces, the main villain Lambda is an all powerful being who was a result of a team of researchers trying to save their planet from wasting away. Lambda was originally a semi-human child, and one of the researchers treated him as his son, being nice to him and teaching him things one would teach a human child. The other researchers felt that Lambda was unsafe, and wanted to destroy him, killing Lambda's only friend in their attempt.
Subverted when Big Bad Lord Brevon from Freedom Planet tries to justify his cruelty and evil schemes with the claim that he's trying to take the Kingdom Stone to save his homeworld. Torque throws his excuse right back in his face, telling him that Brevon's warmongering is the whole reason his home planet is in trouble in the first place.
Red Dead Redemption gives us Jack Marston, the son of the protagonist John. As his father was an outlaw and later a bounty hunter, Jack didn't really see his father, and was mostly raised by his mother and a man called "uncle" (Not related to the family, a friend of John). When he was 16, his father returned once more, promising to stay with them from now on. Several following missions show John doing various stuff around the family farm, such as teaching Jack how to hunt. In the final story mission of the game, the farm is attacked by the same federal agents that John helped to earn his freedom. A firefight starts, and Uncle is killed. Later, John sends Jack and his wife Abigail away from the farm, and realizes that his family's safety is only guaranteed if the soldiers get what they want. John exits the barn, shoots at a few soldiers, and is easily dispatched by the massive firepower of the soldiers. Jack and Abigail return to the farm, and find John's bullethole-ridden body lying on a large puddle of blood. Now the game jumps a few years into the future, with the 19-year old Jack standing besides his mothers grave. From this point onwards, Jack is the playable character, and can be made either a man of honor or a ruthless desperado. Regardless of the player actions, he still has a deep hatred towards Lawmen.