Crossovers
- Ace Combat: The Equestrian War has Black Star and Echo.
- Sympathetic or not, it's undeniable that Aeon Natum Engel's version of the Migou got a valid point for justifying their war against humanity. Namely, about possibly causing a ruckus with their Arcanotech that will wake up certain cosmic horrors, Cthulhu included.
- The Boys: Real Justice: Kimiko realizes that Mr. Freeze is working for Black Mask because the latter is using Freeze's wife as leverage.
- In The Bridge, upon arriving in Equestria and being free from mind control by the Xilians, Monster X is shown to be a Noble Demon. He doesn't bat an eye at killing and is now part of the Big Bad's forces, but if he can manage it, he will go out of his way to avoid harm coming to the defenseless.
- Played With in Dungeon Keeper Ami. The titular character is not a villain by any stretch of the imagination, as expected from one of the heroines from Sailor Moon. However, her goal of returning to her home dimension potentially endangers billions, by allowing the Dark Gods to follow her, and she refuses to be dissuaded. As such the Light reluctantly fights against her in several instances.
- Of further note is Mukrezar. While unquestionably evil, it is a toss-up weather he actually counts as a villain, per se.
- In Origins, avoiding letting the Flood invade through some Negative Space Wedgies created by Faster-Than-Light Travel is generally considered to be a good idea. Killing everyone as a means of accomplishing this is not, landing Sarah in this category, along with several others.
- In the Jackie Chan Adventures and Teen Titans (2003) crossover fic A Shadow of the Titans, Jade is a Anti-Villain. She would rather not be a villain at all, but she hasn't had any luck getting out of it yet.
- Similarly, in the Jackie Chan Adventures and W.I.T.C.H. crossover Kage (a part of Project Dark Jade, like the above), Jade is a villain against her will, having been forced into it by the Guardians' misconceptions and Nerissa's Blatant Lies.
- Dr. Moira Vahlen is this in Stardust. While she comes off, even In-Universe, as a Jerkass Mad Scientist, she does have valid concerns. Twilight Sparkle has so much telekinetic power she's like a walking A-bomb that can detonate multiple times, she can teleport practically anywhere at will, turn invisible and inaudible, perform spells that compel individuals to violently attempt to gain possession of a target she designates, and she seems to just keep coming up with new powers. A hostile Twilight Sparkle would be a nightmare to face. As proven in chapter 33.
- Character Development means she may be climbing out of this position.
- Zack Dawson, the main antagonist in Volume V of the supercrossover military fanfiction series The Terminators: Army of Legend, wants to achieve a peaceful utopia free of war and violence. Unfortunately, the only way he believes to achieve this unreachable goal is to waste any and all fortresses in his path, destroying all militaries throughout the world, with civilian casualties being considered as nameless martyrs in his noble cause.
- In the Evangelion/Warhammer 40,000 crossover Thousand Shinji, Shinji is a manipulative jerkass, makes very questionable things... however his greatest desire is being loved, and he makes bad things to protect or avenge people he cares about.In the end, all I really wanted was someone warm at my side at night. Is that such a terrible thing to wish for? To not be lonely like this, to know that when you go to sleep there will be someone who loves you waiting to smile at you in the morning?
Is that too much to ask?
I would trade it all just to have that again.
- The Bad Life Of Billy The Kid: The Bad Guys are, as the title indicates, criminals with no remorse about stealing, but they are capable of acts of decency, like Shark rescuing a seemingly abandoned child.
- Ashley in 72 Hours starts out as this before her Heel–Face Turn. Like many other students, she's just trying to stay alive, though unlike the overtly Technical Pacifist students, she has no qualms with killing. Indeed, she has an innate streak for sadism and is intent on destroying SABRE from within. Luckily for them, however, her infiltration efforts lead her to realise that she's on the wrong side, and she becomes one of their greatest assets in the end. Not to mention, she winds up the only character who ends the book alive.
- Warlord Kroz is a Type 1 in Tech 10 Rebooted, conducting all of his battles professionally and legally.
- Numbuh 86, along with the rest of the Decommissioning Squad, oddly enough were given the Anti-Villian treatment in Operation:REBEL
. In the story, they seek to capture and Decommission a trio of 13-year-old KND Operatives who are looking for a group of anti-decommissioning rebels called the Kids Eternally There to seek protection from the Squad. The now teenaged Operatives honestly don't see themselves wanting to betray the KND for any reason, but Numbuh 86 is worried that betrayal from escaped teen Operatives would be inevitable and strongly believes decommissioning the 13-year-old Operatives is the only way to assure that doesn't happen.
- Alternate Reincarnation is unclear about which type of anti-villain Kurumi belongs to (just like canon) but Rinne is largely Type IV, as in 'Villain in Name Only.' She does not have a single bad bone in her, actually serves as her friend's conscience at times, and even wishes to see Kurumi being redeemed if possible. Even her goal is simply to find out what connection does she and Shido have.
- Kara in Daughter of Fire and Steel starts off as this. She serves under Zod and doesn't really care about the human race, but she has a strong moral code and actively refuses to kill any humans she fights. She ends up pulling a Heel–Face Turn and joins Superman in the end.
- Light and Ryuk in A Charmed Life. Light really does want to make the worlds a better place and while Ryuk's sense of fun can have rather disastrous results Light concludes it's not done out of any purposeful malice but just because he doesn't know any better.
- Fade: Thanks to knowing how he went Jumping Off the Slippery Slope in the story, Light resolves to never become like his canon counterpart. He sticks to killing only people who have received the death penalty and/or have committed crimes that deserve such a punishment, does not kill anyone who stands in his way, and absolutely abhors the idea of using innocent people to further his own plans. He even refuses to sell out Near to L after figuring out that the former is the one who kills him in the story, as Near has yet to do anything deserving of that fate. While that doesn't change the fact that he is still a Serial Killer, it makes him more sympathetic as it seems he truly does want to make the world a better place. L, on the other hand...
- Callidus Dominus from the Cynical Classicist fanfics, such as "Devotee of Augustus". He is quite aware that he is doing some morally ambiguous things, but justifies this in thinking that benevolent dictatorships are the best form of Government and sometimes gets the Doctor's assistance against greater threats, like the Daleks and Virmok Empire. This goes for other members of the Cult of Augustus and Malphan Empire.
- From the same author is Professor Osmond Stone, from The Sleeping Survivors. While he is kidnapping people and putting them in suspended animation, he is doing it to save the human race, believing eventually an alien attack will destroy humanity.
- From the same author is Professor Osmond Stone, from The Sleeping Survivors
- In the Final Fantasy Tactics A2 fanfic The Tainted Grimoire:
- A character named Crow is this. He is regretful about the evil deeds he did and the author has written him as such. Eventually, he does a Heel–Face Turn.
- Barley as well. He tried to do what was best. It's just that he failed miserably.
- In Alexandra Quick, Benedict Journey and Darla Dearborn are both Woobie, Destroyer of Worlds and Abraham Thorn, if you consider him a villain, is a Well-Intentioned Extremist.
- Harry Potter a.k.a. Tristen Winter in Jaded Eyes Of A Prodigy. His goals ultimately come down to Revenge and not wanting anyone else to suffer as he did under the hands of muggles and so he wipes them all out in planet-wide genocide with a magical Weapon of Mass Destruction. Deep down he just wants the love and acceptance he never received but, thinking this impossible, after his plans come to fruition he fully intends to die.
- The Legend of Spyro: A New Dawn: Deadlock didn't want to be evil and admits that she has her regrets. She's just lost everything, including her sanity, and feels that Spyro and Cynder are responsible for her tragic life, prompting her to attempt revenge. She also feels like her present plan is the only thing she hasn't tried in order to get something extremely important to her. On top of this, she's a very good queen to the Naga and treats them with respect, even being called the best queen they've ever had by some of them.
- Tama and the Interceptor in The Lion King Adventures, both of whom end up changing their ways.
- Game Theory does this with Precia Testarossa, who treats Fate considerably better and also explains her motives to both Fate and Nanoha. Add in a minor incident with Chrono and Nanoha is now working with Precia to help her achieve her goals. Fate is also a somewhat different Anti-Villain than she was in canon, given that her personality is still the same - she just has no reason to change sides.
- In Mega Man: Defender of the Human Race, a story based on the Mega Man (Ruby-Spears) cartoon, Protoman has a policy to not kill, and it's clear that Wily's programming is what makes him unable to defy the doctor. He was also very conflicted over the The Mole part of "Brothers".
- Ballade turned out to be one, as 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 climax of episode 10 he sacrifices himself because continuing with the plan would endanger an innocent human life.
- Mr. Black was revealed as this as more of his back story came to light, as well as his guilt and bad luck with the missions he's assigned.
- Mega Man Reawakened has Woodman, who loves nature and tries to help Robert sort out his anger in the midst of battle.
- It also has Glyde, as he turned to Wily out of having nowhere else to go and showed clear regrets over the matter.
- Dad Villain AU: Thanks to Gabriel's selfish Wish, Sabine suffered the consequences of Emelie's misuse of the broken Peacock Pin, resulting in a world where Tom is using the Butterfly Brooch to seek revenge. Unlike Hawkmoth, however, Viceroy is much more thoughtful and pragmatic in how he uses his powers; rather than openly terrorizing Paris, he proceeds carefully and discreetly, working hard to minimize the impact his search for answers and vengence has upon the city.
- lies of attrition: It's hard to call Chat Noir a villain at all. While he has turned against Ladybug and joined the Big Bad, his reasoning is more than valid given how little he knows. From his perspective, not only did Monarque win, but Ladybug covered up the death of an innocent man (his own father, no less). He's just setting things right. He's also significantly more moral and honorable than Chrysalis.
- Maris Stella: Riodinidae turns out to be Yukari Akimoto, and Paravani is Aron Vector, and the two of them seek the Wish to cure the Akimoto family's Hereditary Curse for everyone's first love to die, which is currently killing Yukari's girlfriend. A hero actually knows this, and despite opposing their villainy, is choosing not to out them as villains — while he opposes their methods and does want them to stop, he doesn't want them to suffer public backlash for what is ultimately trying to save a life.
- Miraculous: Tales of Scarlet Beetle & Ikati Black: Nathaniel Kurtzberg, the Butterfly wielding Monarch, is this in the story. He is kind and caring to his Kwami Nooro and he tries to keep civilian harm to a minimum with his Akuma (especially his classmates and his Love Interest Marc). In one case, he is initially conflicted about Akumatizing his best friend Alix after her family's pocket watch is damaged, but decides to do so to give her a chance at catharsis. And as Monarch, he is polite and asks if she is feeling alright before offering her his power.
- Truth and Consequences: Marinette herself becomes this after a Face–Heel Turn; while her motives for essentially joining Hawkmoth are acknowledged as ultimately selfish anf full of self-justifications, she's never treated unsympathetically. Her main goal is, ultimately, to give Adrien his mother back and protect innocent people from the fallout should Gabriel Agreste's crimes become public knowledge. Between that and making it abundantly clear how much Heroic Fatigue she suffered from during her time as Ladybug, you understand why she's doing it, even as you know it's horribly wrong. The sequel has becoming The Atoner, as well.
- Switchblade has Magne, who may be a member of the League of Villains, and later the Paranormal Liberation Front, but she comes across as much more reasonable and less bloodthirsty than her teammates. After being permanently injured by War Dog in the Battle of U.A, she became a logistics officer and therefore was able to directly see how much the Civil War was costing the PLF and how many of their own people were dying. After Shigaraki's death at Destro's hands, she takes charge of the remaining PLF forces and declares a ceasefire with the Chain, later working out a peace treaty with Nedzu and properly bringing the war to a close.
My Little Pony: Friendship Is Magic
- In Bad Future Crusaders, Babs Seed is a good Royal Guard and believes in the law, but just so happens to work for the oppressive regime of a tyrant who rose to power in a coup.
- Likewise with Crimson Sky, who's a decent family stallion and A Father to His Men, but not only serves Twilight, but also helped enable her coup in the first place.
- Sweetie Belle seems to have become completely amoral, willing to make a deal with the people who killed her family, and not bothering to contact her oldest friends when finding out they're still alive. That being said, she's helped transform the Diamond Dogs from uncivilized brutes to a flourishing society that coexists peacefully with Equestria.
- In Equestria: A History Revealed, General Thunderhide chooses to align himself with the clearly corrupted Nightmare Moon in the Equestrian Civil War, in order to take down Celestia and create a positive change in the world. However, after realizing that Nightmare Moon was crazier than he thought, and knowing that the war was lost with the pegasi's revolt in the west, he surrenders honorably.
- Phaedra from My Brave Pony: Star Fleet Magic III, is one of the few characters to go beyond one trait. Though affiliated with Sombra, she has higher morals than her allies.
- Chasing the Shadow has Orochimaru and Kisame, both of whom, while villainous in inclination, display and act on positive attributes with regard to their friends and comrades.
- A Growing Affection: Gouki Namikaze wants to rule the world, and is willing to enslave (preferably) or kill (if required) all ninjas to do it. But he genuinely believes that he can make the world a better place. He treats his followers with kindness and respect. He loves his wife. And though he will kill if absolutely necessary, he prefers not to, unlike many of the 'good guys'.
- Brave New World: According to Richie, Light of Justice is a type III; a Nice Guy with a noble goal who wants to be Richie's best friend. He just happens to be a Knight Templar. Thus, it isn't surprising that he is the reincarnation of N, King of Team Plasma. Also, when the Light of Justice hears of the true extent of the Nihilator's crimes, he wants to put aside the gathering of Arceus' plates to focus on the Nihilator's destruction, and is certain that his organization and Team Getem can put aside their conflict to defeat an organization that is truly evil.
- Pokémon Reset Bloodlines: The resident Knight of Cerebus, Belladonna Tyrian and her girlfriends are this. As Bloodliners, they consider themselves above humanity and thus have little regard for the law, but their typical actions are usually just breaking into places and theft, the sole exception being the events of Chapter 23, and even then they had standards. In the end, they're a group of lovers that typically act more like teenagers wanting to have fun, only going worse when someone harms one of them.
- Murderer's Row: This applies to a good chunk of the cast, considering that it takes place in prison.
- Church is a ruthless criminal and blackmailer who will do anything to keep a leg up, and a total Jerkass in general. However, he has his own moral code, prefers to stop things from escalating to violence, and cares deeply for those close to him.
- Tucker is a con man who prides himself on manipulating people, but his Papa Wolf tendencies and his guilt over some of his crimes (such as robbing Connie, kidnapping Pillman's foster son, and inadvertently driving Jones to suicide) serve to make him sympathetic.
- Grif and Simmons are generally fairly benign prisoners who rarely bother anyone and spend most of their time bickering amicably and hanging out with the other residents of the Row. They are, however, far from harmless, and harming anyone they care about leads to a brutal beating if you're lucky and death if you aren't.
- Lopez is only in prison for killing someone who threatened to murder his beloved wife Sheila, and he generally spends most of his time snarking at the other prisoners and checking up on her. He still admits that he'd kill anyone should it keep Sheila safe, and he temporarily served as The Dragon to O'Malley and (unwillingly) helped him mutilated Donut, the prison's Token Good Teammate.
- Caboose was left brain damaged in a car accident, leaving him with the mind of a child. As a result, he's gullible enough to be easily manipulated into killing and maiming at the behests of anyone in his good graces.
- Flowers is a ruthless henchman for the Director and not all there, but he's also Affably Evil and genuinely committed to helping inmates reform in his own way.
- Miller is a ruthless gang leader, but he's motivated by a desire to avenge his friend Jones, who Tucker had indirectly and inadvertently killed, and he's not really any different morally from Church and Tucker. This lessens after he's sent back to prison, at which point he becomes far more vicious and cruel.
- Pillman is a violent career criminal, but he's loyal to his employers and underlings and is a loving father.
- Similarly, his son Sharkface is just as violent, but he's also a surprisingly friendly Cloudcuckoolander who's very easy to get along with.
- Notably averted by O'Malley, who's just a sadistic sociopath all the way through with no redeeming qualities.
- Children of Remnant: The Schnees and the Belladonnas are on the verge of starting a war due to their vengeful desires, yet they're grieving family members mourning the loss of their children, so it's hard to not feel sorry for them.
- A Rabbit Among Wolves: The White Fang branch Jaune accidentally takes control of are terrorists, but they were driven to crimes by the injustices they suffered. While Jaune is trying to reform them, he does find himself agreeing with them that the injustice they've endured is beyond horrific.
- Ruby and Nora:
- Like in canon, Emerald is loyal to Cinder (even more so here because they’re also lovers), but is horrified and conflicted by what Cinder makes her do.
- Leonardo was already pretty sympathetic (or pathetic) in canon. Here, Salem is holding his wife and child captive, forcing him to help or she’ll have them killed painfully.
- RWBY: Dark: Yang Xiao Long never wanted to be evil, but had her mind broken and and twisted by Ruby, and will now kill at Ruby's command.
- Vale's Underground: Hazel is the only criminal in the entire work with a sympathetic character and motivation. Yes, he’s assisting an organ harvesting operation, but only so he can save his sickly and dying daughter.
- Many of the villains in Forum of Thrones, have at least some sympathetic traits and good intentions.
- Maron Mullendore is hardly a sympathetic man once his true identity is revealed. A cruel sadist with a fondness for mind games and brutal torture methods, as well as the fact that he won't even back down from harming children makes him one of the most despicable villains in the story. However, even then he retains some of his knightly virtues, like a sense of honour, as twisted as it is. His ultimate goal is also positive, making him a Well-Intentioned Extremist.
- The Burned Man is only a villain if you stand against him and even then, he has only few truly villainous traits. He is genuinely concerned for the future of Oldtown, even if he uses criminal methods to achieve this future. He is also by all means a genuinely polite man who is friendly unless provoked. That does not mean that he is not capable of some pretty evil things, but all in all, he still hardly qualifies as a villain.
- Harris Flowers. Despite his noble demeanor and trying to appear as friendly as possible, he is an unstable Control Freak who quickly resorts to violence when things don't go his way and who has problems controlling his urges. He is also a strong, generous and just leader with a natural talent for ruling. Ultimately, his goals are absolutely well-intentioned, but it doesn't change the fact that he is willing to murder others to achieve it.
- Jaylon Gordus is a very tragic figure. A rude Jerkass of a man, he comes from a dysfunctional family, with a depressed and abusive father, from whom he ran away. Stranded in Oldtown, he long since realized that he is doomed to a life he does not want to lead, fighting for a man he does not want to fight for, but left with no alternatives. This turned him, once idealistic and proud, into a cynical jerk. However, he reveals his more likeable side when he temporarily joins up with Samantha to save Lucas, first out of necessity, but later on out of genuine affection for her and the others, showing that not all of his former self is lost.
- In the Alternate Universe Fic Prison Island Break, the protagonists are barely even Designated Heroes. Their goal to escape prison isn't particularly noble; all admit guilt, and most intend to commit more crimes on their escape. Their crimes include murder, rape, bank-robbery, fraud on a global scale (Tails claims to have nearly made himself the sole owner and stockholder of Sony), escaping other prisons, and what boils down to terrorism. It's the Morality Kitchen Sink. However, since the story is told mostly from their perspective, Sympathy for the Devil ensues to some degree.
- Lord Maledict from Sonic X: Dark Chaos is definitely this, mostly due to his strong Pragmatic Villain tendencies. In fact, most of the "villain" characters in the story are this, minus some of the obvious evil characters like Beelzebub and Muhammad.
- Jimmy Osgood is a type II in Jimmy's Visit With Dr. Franklin, he had to watch his own brother being tortured until he died all because of Ebon's paranoid belief that they were part of a rival gang and thought that he was responsible for his brother's death because he told Ebon that he had a twin brother so he felt like he had to make it up for him by bringing him back to life via The Quantum Vapor, only to end up hurting one of his friends, Richie.
- In Black Wings, Black Sails, Laurence aims to free as many slaves as he can by capturing slaving ships and attacking slave ports. By Chapter 3, he winds up joining forces with the Tswana, after finding that many of the slaves he's rescued originate from their kingdom. Deplorable as the trade may be to us modern readers, it still supports a lot of livelihoods and all of the labor from the trade results in unprecedented agricultural productivity that drives the First Industrial Revolution. This contrast is underscored when Laurence slits a slaver's throat without remorse, prompting Granby's horrified reaction and remark that Laurence just killed a man in cold blood.
- In the Anomaly (Series), John A. Pence is discovered to be this after it's revealed that the Anomaly was using him as a puppet, and in reality he had far less extreme goals before being hacked by the Anomaly to replace Frisk as the player character.
- A running theme in Bird is the traditional Hero/Villain roles. In the world of Earth Bet Heroes and Villains work on principles of Grey-and-Grey Morality, with Villains being the Designated Antagonist role and not always unsympathetic, or even evil. This is subverted in Bird, where most of the patients at Alchemilla come from both sides of the fence but nearly all of them are sympathetic, and dangerous.
- In A Darker Path, Atropos is a multiple murderer who not only explains who she's going to kill and when, but confirms afterward that it was really her. However ... her victims are invariably vicious supervillains who kinda deserve it (or at the very least didn't heed her warning).
