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  • Child of the Storm and its sequels have several examples.
    • The Winter Soldier a.k.a. Bucky Barnes, in Child of the Storm, isn't personally evil, but has very little control over his actions at first because of the sheer scale of his programming and his amnesia, with the corresponding loss of identity. As it starts to wear off and his memories start to come back, he does his best to sabotage his missions and preserve as many lives as possible, but he's still vulnerable to being brainwashed again. At the end of the book he is ultimately freed of his brainwashing and resumes his life as Bucky Barnes, albeit with all the knowledge and skills of the Winter Soldier.
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    • The Dark Phoenix, in Ghosts of the Past, is the result of a Phoenix host ( Harry) having six months of horrific memories, including physical and psychic torture, dumped on them at once. This leads to a vengeful rampage, with the signature Phoenix scream being consistently described as 'agonised', and the entire section being characterised as a traumatised child lashing out. Thankfully, they're talked down via the Power of Love.
    • The original Dark Phoenix, Surtur, was a Well-Intentioned Extremist and Visionary Villain who wanted to make a better universe, and was not talked down - end result? He ate a galaxy.
    • Rachel Grey/Maddie Pryor, who was kidnapped and had her death faked practically at birth by Essex/Sinister, so that he could raise her as his personal enforcer. All while experimenting on her, telling her she's a tool and not a person (and treating her as such), and giving her zero emotional support. This causes her to grow into an emotionless shell of a person with no understanding of anything like compassion or love, to the point of willingly going along with what she knew was initially faked affection by Gambit who was, originally, planning to use her to escape (he changed his mind on getting to know her), and outright breaking down when confronted with genuine kindness and concern, because she just doesn't know how to deal with it. Harry treating her like a person, and learning her true origins, causes her to have a Heel–Face Turn.
  • In Mega Man: Defender of the Human Race, Proto Man was stolen and reprogrammed early in life. As a result, he can't defy Dr. Wily's orders even when he really wants to, such as being a Heel–Face Mole or abandoning a life-threatening situation.
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    • Ballade is also this. He realized that being the robot Wily's most proud of meant others will fight for the spot, and while he showed respect to his enemies he got no respect from comrades.
  • In The Tale of Discord, well, DISCORD OF ALL PEOPLE is this. Let me count the ways. His father was disgusted by his appearance, barely anyone treated him like a normal citizen, his crush (Celestia) didn't return his feelings (though they didn't exactly hate each other back then), and then these events happen: his best friend, Luna (the mare he now knows he loves) feels that Discord betrayed her and she leaves him in tears. This is only the first part of his Start of Darkness. He later learns that his doting and ailing mother died giving birth to his sister (who would begin the line of the Sparkle family. Well, whaddya know?). This sends Discord on his path of chaos (but not before taking care of his dad.) If that doesn't make it any sadder, it is revealed that the spirit of Nightmare Moon was possessing him and judging by his behavior nowadays, he is permanently scarred by his past. By the end, you just want to give him a hug!
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  • Aftershocks turns J.D., the Ax-Crazy Serial Killer from Heathers into one. In this AU fanfic, he attempted to take his violent urges out in a legal way by joining the army, but came back with thorough PTSD, suffering violent flashbacks and nightmares. By the time he returns home, he sincerely wants to just settle down with Veronica and their twin daughters and have a normal life, but his constant flashbacks and unstable mind make him a danger to his children. At that point, he's less evil and more broken and pitiful.
  • Fade manages to turn Light Yagami into this. In this story, he was blackmailed into becoming Kira by Ryuk to help find a rogue Death Note, and even after he embraced the role he goes through great pains to not become like the original Kira — he kills only those are on death row or have committed crimes deserving of it, takes absolutely no pleasure in killing, and refuses to involve innocents, let alone kill them. He even hates manipulating people, despite being so good at it. And then L comes into the picture. L frames him, holds him captive for weeks, and even psychologically tortures him by faking Kiyomi's death to get Light to confess. However, since L was the only contact throughout all that time, Light develops Stockholm Syndrome and becomes completely dependent on him. Which is a problem, as while L does care for him, L is also the holder of the rogue Death Note and has become a monster far worse than canon!Light at his most heinous. Light, however, is too attached to him to see it. At that point, it's not hard to see Light as not a villain but instead another victim, which is part of why Beyond is so intent on saving him.
  • Yugioh EQG: Shadow Gates: Shadow was a Duel-Bot that was programed to adapt to duels the same way a human would, but somehow gained sentience on his own. He hid this from almost everyone, out of fear that they would experiment on him. He only revealed it to his creator Sombra, who he trusted above all else and saw as his father. Sombra was eventually convinced Shadow was alive, so he scrapped the project and hid Shadow away in the deepest server of Freeze Industries. Shadow dreamed of being human as he slept, and when Sombra woke him years later he promised to fulfill that dream if Shadow helped him accomplish his goal. So Shadow became a ruthless duelist that hurts his opponents in battle, all to one day be human. However, this dream never came true, and he was destroyed in his duel with Flash Sentry in the finals of the Celestic Cup.
  • Christmas With Eggman makes Ivo Robotnik from the Sonic games this by making his family not only overbearing but disappointed that he isn't as talented as a villain as they'd hoped. What's really telling is that even Sonic says, after first encountering them, "You know... I used to wonder what drove Eggman into villainy... Not anymore!..."
  • In Marionettes, both Director Masquerade and her maid/bodyguard Miss Marshmallow are this:
    • Masquerade's mother was an Abusive Parent who raised her from birth (or possibly from being cloned with the Foal Making Mirror for the expressed purpose of such) to be an emotionless Sociopath completely dedicated to her role as director with no choice at all beyond that, to the point of actively brainwashing her until she lost any ability to feel anything at all. Even Trixie acknowledges despite all the pain Masquerade caused her and the other Marionettes, that she can't be angry at Masquerade because she never had a choice at all and is as much a victim as the Marionettes. Also applies to her mother, who implies her treatment by her own mother was no better. In the end, Masquerade goes completely catatonic due to being unable to function without leading the Stallions since that's all she's lived for since she was born.
    • As for Marshmallow, she's a special Marionette specifically made and programmed to not feel most of her emotions except happiness and to be extremely child-like so that she can't comprehend her actions are wrong. She was Masquerade's only true friend as a child, but Masquerade gradually was stripped of any capacity to return her friendship thanks to her mother. In the end she dies for Masquerade, but Masquerade's emotions are so far gone she can't even mourn her, something Trixie pities Masquerade for.
  • Apotheosis (MHA): The Villain Protagonist, Midoriya Izuku. When it comes down to it, Izuku is a scared child who loved heroes and wanted to help people, only to have his dreams crushed by his idol and intentionally and unintentionally ostracized and marginalized by all the important people in his life because he was a Muggle Born of Mages in a world where Everyone is a Super. Several people, such as All Might (the aforementioned idol), All Might's successor Mirio, his friend (and potential Love Interest) Ochaco, and his mother Inko, still see good in him and want to redeem him, but as far as Izuku is concerned, he's too far gone to stop now.
  • Himiko Toga in The Undead Schoolgirl: Dead Pulse became a serial killer due to undiagnosed and untreated Quirk Instability. Some theorize she could turn over a new leaf if she got proper therapy.
  • The Ouroboros makes the original turtles, April and Casey that the 2012 series followed into this by exploring the implications of their actions at the end of the Space Arc. Namely, the fact that they traveled back in time to Set Right What Once Went Wrong... but instead of fixing their own reality, effectively created an Alternate Timeline. The turtles, April and Casey native to this reality then head off into space while the 'originals' assume and take over their lives. While they are deliberately deceiving their counterparts, telling them that they have to maintain a Stable Time Loop that doesn't actually exist, they're doing so out of the belief that this is the only way to reclaim the lives they left behind.


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