[[AC: ''Literature/BattleRoyale'']]
* Ashley in ''Fanfic/SeventyTwoHours'' starts out as this before her HeelFaceTurn. Like many other students, she's just trying to stay alive, though unlike the overtly TechnicalPacifist students, she has no qualms with killing. Indeed, she has an innate streak for sadism and is intent on destroying [[LaResistance 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. [[spoiler: Not to mention, she winds up the only character who ends the book alive.]]

[[AC: ''WesternAnimation/BenTen'']]
* Warlord Kroz is a Type 1 in ''FanFic/Tech10Rebooted'', conducting all of his battles professionally and legally.

[[AC: ''WesternAnimation/CodenameKidsNextDoor'']]
* [[WesternAnimation/CodenameKidsNextDoor Numbuh 86]], along with the rest of the Decommissioning Squad, oddly enough were given the Anti-Villian treatment in ''[[http://www.fanfiction.net/s/6314936/1/Operation_REBEL Operation:REBEL]]'' In the story, they seek to capture and [[BrainWashingForTheGreaterGood 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 honest 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.

[[AC: CrossOver]]
* ''{{Fanfic/AceCombatTheEquestrianWar}}'' has Black Star and Echo.
* Sympathetic or not, it's undeniable that ''FanFic/AeonNatumEngel'''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.
* Played with in ''FanFic/DungeonKeeperAmi''. The titular character is not a villain by any stretch of the imagination, as expected from one of the heroines from [[spoiler: Anime/SailorMoon]]. However, her goal of returning to her home dimension potentially endangers ''billions'', by allowing the [[GodOfEvil 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 the ''WesternAnimation/JackieChanAdventures'' and ''WesternAnimation/TeenTitans'' crossover fic ''Fanfic/AShadowOfTheTitans'', Jade is a [[SlidingScaleOfAntiVillains Type IV]] AntiVillain. She would rather not be a villain at all, but she hasn't had any luck getting out of it yet.
** Similarly, in the ''WesternAnimation/JackieChanAdventures'' and ''WesternAnimation/{{WITCH}}'' crossover ''Fanfic/{{Kage}}'' (a part of ''FanFic/ProjectDarkJade'', like the above), Jade is a villain against her will, having been forced into it by [[NiceJobBreakingItHero the Guardians' misconceptions]] and Nerissa's BlatantLies.
* In ''FanFic/SovereignGFCOrigins'', a ''MassEffect''[=/=]''StarWars''[[spoiler:[=/=]''[=Borderlands=]''[=/=]''[=Halo=]'']] MassiveMultiplayerCrossover, avoiding letting [[spoiler:the Flood]] [[AlienInvasion invade]] through some [[NegativeSpaceWedgie Negative Space Wedgies]] created by FasterThanLightTravel is generally considered to be a good idea. [[KillEmAll Killing everyone]] as a means of accomplishing this is not, landing Sarah in this category, along with [[KnightTemplar several]] [[WellIntentionedExtremist others]].
* Zack Dawson, the main antagonist in Volume V of the supercrossover military fanfiction series ''FanFic/TheTerminatorsArmyOfLegend'', 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 ''FanFic/TheBridge'', upon arriving in Equestria and being free from mind control by the Xilians, Monster X is shown to be a NobleDemon. He doesn't bat an eye at killing and is now part of the [[BigBad Big Bad's]] forces, but if he can manage it he will go out of his way to avoid harm coming to the defenseless.
* In ''Evangelion''/''Tabletop/{{Warhammer 40000}}'' crossover ''Fanfic/ThousandShinji'', 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.

[[AC: ''Manga/DeathNote'']]
* Light and Ryuk in ''FanFic/ACharmedLife''. Light really does want to make the world[[spoiler:s]] a better place and while Ryuk's sense of fun can have rather disastrous results Light concludes it's not done out of any [[NonMaliciousMonster purposeful malice]] but just because he doesn't know any better.

[[AC: ''Series/DoctorWho'']]
* Callidus Dominus from the Cynical Classicist DW Fanfics, such as [[https://www.fanfiction.net/s/10630391/1/Devotee-of-Augustus 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 [[https://www.fanfiction.net/s/9830239/1/The-Sleeping-Survivors 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.

[[AC: ''Franchise/FinalFantasy'']]
* In the FinalFantasyTacticsA2 fanfic FanFic/TheTaintedGrimoire:
** A character named [[spoiler: Crow]] is this. He is regretful about the evil deeds he did and the author has written him as such. Eventually, he does a [[spoiler: HeelFaceTurn]].
** [[spoiler: Barley]] too. He tried to do what was best. It's just that he failed miserably.

[[AC: ''Franchise/HarryPotter'']]
* [[ThatManIsDead Harry Potter a.k.a. Tristen Winter]] in ''[[FanFic/TheJadedEyesSeries 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 [[spoiler: and so he wipes them all out in planet-wide genocide with a magical WeaponOfMassDestruction]]. Deep down he just wants the love and acceptance he never received but, thinking this impossible, after [[NoPlaceForMeThere his plans come to fruition]] [[DeathSeeker he fully intends to die.]]

[[AC: ''VideoGame/TheLegendOfSpyro'']]
* Deadlock, the BigBad of [[Fanfic/TheLegendOfSpyroANewDawn The Legend Of Spyro: A New Dawn]]. She 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.

[[AC: ''Disney/TheLionKing'']]
* Tama and the Interceptor in ''Fanfic/TheLionKingAdventures'', [[spoiler: both of whom end up changing their ways.]]

[[AC: ''Franchise/LyricalNanoha'']]
* ''Fanfic/GameTheoryFanFic'' does this with Precia Testarossa, who treats Fate considerably better and also explains her motives to both Fate and Nanoha. Add in a [[PoorCommunicationKills 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.

[[AC: ''WesternAnimation/MegaMan'']]
* In ''Fanfic/MegaManDefenderOfTheHumanRace'', a story based on the WesternAnimation/MegaMan 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 HeelFaceMole 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.
* ''FanFic/MegaManReawakened'' 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.

[[AC: ''WesternAnimation/MyLittlePonyFriendshipIsMagic'']]
* In [[FanFic/EquestriaAHistoryRevealed Equestria: A History Revealed]], General Thunderhide chooses to align himself with the clearly corrupted Nightmare Moon in the Equestrian Civil War, in order to [[NecessarilyEvil take down Celestia and create a positive change in the world.]] However, [[spoiler: 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 ''[[FanFic/MyLittleUnicorn 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.

[[AC: ''Franchise/{{Naruto}}'']]
* ''FanFic/AGrowingAffection'': Gouki [[spoiler: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'.

[[AC: ''SonicTheHedgehog'']]
* In the AlternateUniverseFic ''[[Fanfic/PrisonIslandBreak Prison Island Break]]'', the protagonists are barely even [[DesignatedHero 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 MoralityKitchenSink. However, since the story is told mostly from their perspective, SympathyForTheDevil ensues to some degree.
* Lord Maledict from FanFic/SonicXDarkChaos is definitely this, mostly due to his strong PragmaticVillain tendencies. In fact, [[BlackAndGrayMorality most of the "villain" characters in the story are this]], minus some of the obvious evil characters like Beelzebub and Muhammad.