"Of all tyrannies, a tyranny exercised for the good of its victims may be the most oppressive. It may be better to live under robber barons than under omnipotent moral busybodies. The robber baron’s cruelty may sometimes sleep, his cupidity may at some point be satiated; but those who torment us for our own good will torment us without end for they do so with the approval of their own conscience. They may be more likely to go to Heaven yet at the same time likelier to make a Hell of earth."
A villain who is convinced that his actions are acceptable or helpful. These villains aren't justifying their wrongdoings. They aren't compelled by unnatural forces. They just don't comprehend that they're doing anything wrong. This can be achieved in several ways:
They may not be privy to The Masquerade and thus not know their actions would cause damage.
They will be confused or annoyed at any explanation that what they're doing is wrong, and react with confusion or disdain if the heroes disagree with them.
A horror trope (and occasionally a comedy trope in a Black Comedy), this can really freak people out if played right. It places the heroes into a situation where they can't even try to reason with the villain. It can also be used to underscore that the villain is indeed a tragic figure, as he or she (or it) may never have actually intended to harm anyone. Alternately, this can be used to make a creature sympathetic. You give it a valid reason for doing the things it does, and once it has that reason, it won't see what it's doing as wrong.
There are two basic requirements for a character to be this trope:
They are dangerous. The character is quite capable of causing tyranny, tragedy, chaos, wanton destruction, etc., and has done so on numerous occasions. Contrast the Ineffectual Sympathetic Villain and the Minion with an F in Evil, who represent relatively minor threats to the protagonists.
They have no idea that they're doing anything objectionable. In their eyes, their actions are either good or simply harmless. Even if they recognize that something is wrong, they won't realize that they are the problem, and if they do, they might not realize the scale of their actions. For example, a Sex Is Evil and I Am Horny character might sexually assault women and feel as if he's their victim.
Russia in Axis Powers Hetalia doesn't seem to realise there's anything wrong with the way he treats the other Soviet nations; on one occasion, he asks Latvia why he's so small, receives the response that it's because he keeps pushing him down, and then tries to help by stretching him. He was driven to madness by Bloody Sunday.
One interpretation of Mao from Code Geass is that he honestly believes that the people he goes after deserve the punishment he hands to them.
Hansel and Gretel from Black Lagoon qualify. Children emotionally/physically/sexually abused into insanity, they see no problem with being cruel and sadistic murderers because, in their minds, that's how the world works.
Misa Amane. Unlike her boyfriend Light, she doesn't even try to rationalize her actions; it simply never occurred to her that murdering tens of thousands of people is wrong. Or her love/lust for Light distracts her. Mind you, she was killing people just to meet Kira before she even knew it was him. Her childishness, which is even greater than Light's, makes it hard to tell what really makes her tick.
Light himself is one as well. How obvious is it when he's trying to make the world a better placeby killing. When Light says he plans to kill all the evil people in the world, Ryuk says "Then you'd be the only evil person left." Light says he doesn't understand what Ryuk means.
The Digimon Emperor from Digimon Adventure 02 is a Jerkass, but he genuinely thinks the Digiworld is just a game, so there is nothing wrong with playing the bad guy. When he realizes his mistake, he pulls a Heel-Face Turn and becomes a powerful ally for the heroes.
Likewise, in Digimon Xros Wars, Yuu Amano is manipulated into thinking the digital world is just a game world where he can play to his full potential without actually hurting anyone. Finding out the truth hits the poor kid hard, but thankfully, the rest of the kids rescue him and are willing to forgive his mistake.
It could be argued that in Digimon Tamers The D-Reaper is this, as it's just a program that was originally designed to prevent other programs from exceeding their parameters by deleting them, so it only sees the Digital World as a mass of excess data to be deleted. The part of the D-Reaper that possess Jeri, escapes into the real world, and develops a malicious self-awareness however...
Even that part appears to simply have reached the conclusion that humans actually crave obliteration deep in their hearts after reading the mind of a very depressed young girl.
In Dragon Ball Z, Majin Buu's first form, Fat Buu, doesn't really know that killing millions of people is wrong. He even turns an old man into milk as a gift for a small child because the child complimented him. Mr. Satan actually turns him into a good guy temporarily just by explaining to him that it's bad to kill people. Then, just as it looks like the Fake Ultimate Hero has actually saved the world, someone shoots Mr. Satan and his pet dog. Buu doesn't take it well. Justified because Bibidi (Babidi's father) made him to destroy, and that's all anyone ever ordered him to do. Mr. Satan was the only one that even took the approach to explain it to him, after Bibidi and Babidi were both dead.
Turns out this was basically a Thanatos Gambit made by the previous Guardian of the entire Universe (who looked like a Palette Swap of Fat Buu). When Buu was first created, the Guardian saw that he was too powerful to defeat with direct confrontation and so allowed Buu to absorb him (a negligible power boost for the monster itself) so that his own purity and innocence would overwhelm the incredible malice and hatred the creature possessed. This is what made it possible for Mr. Satan to reason with him. When Super Buu "purifies" himself of everyone he's absorbed, he reverts back to Kid Buu, slightly less powerful, but dangerously more insane and malevolent. Unlike any of Buu's previous forms, he has no dialogue (no playful songs, no one-liners, no monologuing on his superiority) except for maniacal laughter as he kills people and blows up planets for fun.
Not so much. Kid Buu was mentioned as insane from the start and killed because Babidi told him to. The key difference was that Kid Buu was more malicious and took sadistic pleasure in killing where as Fat Buu had absorbed not just Daikaioh's powers and abilities but also his purity and innocence, making Buu more like a child than a single-minded sadistic killer. Daikaioh was shown to be surprised when Buu survived his attack and likely his absorption was unintended, but had a positive outcome at his sacrifice.
The Claw from GUN×SWORD. Even though he has a history of killing people, he comes across as a really nice old guy, and after you actually watch him kill someone onscreen, it's still hard to see the man as a villain. Even his ultimate plan is arguably noble in intent, but it isn't until his Villainous Breakdown towards the very end do you even get the feeling he might actually be evil, and it's so brief that it's still hard to believe.
The Vajra in Macross Frontier cause significant damage and many deaths to the Frontier colony because their Hive Mind and method of communication means they're unable to understand the concept of individual beings, or even that most of the humans are even intelligent, with their attacks being an attempt to reach the sole person who seems familiar to them. When Ranka manages to figure this out and how to use her connection to communicate the idea to them, the Vajra immediately start fighting to save human lives, even sacrificing many of themselves.
The ELS from Gundam 00 Awakening Of The Trailblazer. Humanity defends itself from them because these flying hunks of living metal keep trying to absorb and transform humans. It later turns out that the ELS were not being malicious: they were simply trying to communicate with and understand humanity, and the most efficient way they knew to do so was to combine physical forms and share consciousness. Once the ELS realize why they're being perceived as hostile, they stop immediately, and begin finding alternate methods of communication.
JoJo's Bizarre Adventure: Enrico Pucci is a priest who believes himself to be doing the will of God. Said will involves killing everyone, destroying the world, and then remaking it without the protagonists ever being born, in addition to making all people know exactly how their lives will unfold and how they will die. Supposedly, this would make a perfect world where humans would no longer use free will to hurt each other.
Jellal from Fairy Tail, in the arc where he appears. He seems to genuinely believe that he's doing the right thing, but what he's trying to do is bring the story's Bigger Bad back from the dead. That he kills one of his former friends, enslaves hundreds (albeit without them realizing this) and psychologically tortures his love interest before trying to use her as a sacrifice don't clue him in to the fact that he's on the wrong side. It does help that he was Brainwashed and Crazy at the time, but later chapters have painted this less as total control and more as giving him the motive and letting him handle the rest.
Fran Madaraki of Franken Fran is a Mad Scientist and Frankenstein's Monster who believes that a life must be saved no matter what, and does not understand the concept of a Fate Worse than Death. She does often do genuine good, but performs some truly horrific procedures to keep people alive. She genuinely thinks that she is helping and is offended whenever someone criticizes her methods.
Paradoxically, she is also very concerned about overpopulation. When a clone she creates begins reproducing asexually too quickly, she kills all these innocent, sentient clones except for one. She reasons that so long as one copy of the person exists, she has not truly killed anyone.
Infinite Tsukuyomi turns out to be this in Naruto. Even before it was revealed that Infinite Tsukuyomi turns its helpless victims into Zetsu's, it was a technique designed to imprison and Mind Rape an entire world with 'good dreams'. Madara and Obito never thought, not even once, that it'd be Too Good To Be True and went through with the plan, the former for his own Ego, the latter so he could experience the fantasy of Rin being back.
Humpty-Dumpty from Arkham Asylum: Living Hell: obsessed with fixing objects he perceived as broken, he "took apart" his abusive grandmother to see what made her so mean, not realizing that she couldn't be put back together again. Not for lack of trying, of course — he stitched her back together with bootlaces.
From the same city: Harley Quinn doesn't seem to be truly evil herself, but will gleefully do anything that her "puddin'", the Joker, asks of her, regardless of who gets hurt. It's an unhealthy relationship, to say the least, and (this is the worst part) they wouldn't have it any other way. Although it varies with Harley; sometimes, she's oblivious to what she's doing, sometimes, she knows exactly what she's doing and doesn't care. The Harley Quinn comic mixes both.
Bizarro in The DC Universe often has this problem, depending on which version you're dealing with. Often, he'll try to do good but have no concept of how destructive his own strength is and cause more collateral damage than help, or he'll actively blow things up because his "save/destroy" wires are crossed.
The Bogeys in Fungus the Bogeyman travel to the surface of Earth every night to frighten, pester, and otherwise disturb the human "drycleaners" who live there. The Bogeys get no pleasure from this and gain nothing from it. In fact they've got absolutely no idea why they do it. It's just what Bogeys do.
Lenore from Lenore the Cute Little Dead Girl accidentally kills people and animals on a regular basis, but seems a bit too clueless to grasp what she's actually doing. She realizes once what she had done throughout the comic, and is thoroughly shocked, while playing with a cute living girl. She ends up accidentally killing her by being too overwhelmed to pay attention to what she was doing.
Jei, in Usagi Yojimbo. He views his actions as cleansing the world of sin, and even adopts an orphaned girl! That said, just as many of his victims seem to be innocent (or at least not actively evil) as not. Added to that, he obsessively hunts down Miyamoto Usagi, a virtuous and noble individual. Subsequent hosts of the darkness inhabiting him seem to have even more broken, warped views of the world's morality.
The title should have been a dead giveaway, really.
Celestia from The Conversion Bureau: Not Alone turned out to be this. She genuinely thought that converting humans into ponies was the right and proper thing to do, because she found humans to be inherently evil and decided it would be moral to turn them into creatures of 'good.' Granted, this still makes her a major racist, but not malicious.
Cupcakes: Pinkie Pie just wants to throw Dash a party! Specifically, a demented-serial-killer-murders-you party! Isn't it fun being maimed, killed, and eaten?
Fluttershy in Pattycakes doesn't seem to realise that psychologically and chemically mind-raping Dash until her spirit breaks and she becomes convinced that she's Fluttershy's baby is in any way unethical. Sure, she was breaking her own rules involving her mental regression serum — specifically, the one about only using it consensually — but she wanted to be a mother so badly and, well, regressed!Dash is so happy to be a foal again, how could that be wrong? And making Scootaloo run a course of insane "tests", well, Scootaloo will either come out of it happy and well-adjusted as Dash's new adopted big sister (Stockholm Syndrome is a real bitch, isn't it?), or she'll come out of it happy with her mind almost totally destroyed as her little sister! Win-win!
After having her body destroyed, something happens to her to make her start questioning her logic. During her next fight against the heroes (after she takes over Sparkler's body), she stops to wonder if she is wrong. Before Fluttercruel can decide for herself though, Rancor betrays Discord. This distracts Fluttercruel from her thinking, and makes her forget about it.
Another example from the same fic is Tom, a Golem born from Dark World!Rarity's Element of Desire reacting to her desire for the bolder Discord tricked her into think is a diamond (which she now believes is her husband) to be alive and making it come true. Tom, being only a few seconds old at the time, genuinely doesn't know any better than what his mother tells him to do, which at the time is 'protect' her from the mane six's attempts to redeem her. They end up having to kill him to save her, something which is treated tragically due to this trope.
A few of the villains in The Otherworld Anthology are like this. The American McGee Jabberwock blames Alice for Wonderland's corruption and believes destroying her will restore the world. The Queen of Trolls is trying to destroy humankind as she believes it'll help her people and will be justice for what Peer Gynt did to her. The anthology's version of Mr. Whiskers thinks he's helping Brandy and Lola live better lives by changing them from humans into, respectively, a dog and a snake, and keeping them in Otherworld under the Hatter's regime.
In Necessary To Win, Oarai faces Saunders in the semi-finals; not only is Saunders as generally fun-loving and friendly as in canon, but they also have several of Nodoka's old friends, who have come this far for a chance to see her and face her in a tankery match again. Unfortunately, if Saunders wins, Nodoka will have to leave Oarai for a new school (Saki canon), Miho will be disowned (from the Girls und Panzer manga) and Oarai will shut down (both from the Girls und Panzer manga and anime), none of which Saunders wants to happen.
In Seventh Horcrux, it's repeatedly pointed out that when Hermione starts breaking the rules, she also throws away her morals. Notable examples are her plan to brew an illegal potion (Polyjuice potion) using stolen ingredients so she could knock out some members of Slytherin, replace them, and interrogate Draco Malfoy in the Slytherin common room, her adding a punishment clause to the DA contract without telling anyone, and her obliviating her parents and sending them to Australia. There are other examples in the fic, but the examples listed here are notable for being things she canonically did in the series. Despite this, Hermione doesn't understand why Harry thinks she's evil, and usually takes offense to the accusations.
Lampshaded in A Charmed Life when Ryuk recognizes that Light does not consider himself to be evil and to hint at such would only serve to upset and anger him.
Film — Animation
In the 2007 Film adaptation of Beowulf, Grendel has no problem killing humans because the sound of their parties causes him intense pain.
You could argue that the humans themselves fit this trope for causing Grendel pain in the first place.
The humans in Finding Nemo. Making things worse, all the things they do are stuff that humans in Real Life do normally. Darla in particular — she doesn't understand that shaking the bag kills fish and she seems genuinely happy to get a new pet.
How to Train Your Dragon: Stoick the Vast isn't evil by any means (in fact, he is quite The Good King) but his actions still fall under this. He believes he's doing the right thing by disowning his son and attacking every dragon in sight. But it's his bad temper and staunchtraditionalism that almost gets his tribe slaughtered in the film's climax. (Until they're saved by his son- Hiccup- and a pack of dragons.)
This carries over in a lesser form to Stoick's parenting. He's a neglectful father, but not because he dislikes Hiccup. It's because he has no idea how to connect with the boy (they are very different people).
The Hunchback of Notre Dame: Judge Claude Frollo. He is The Fundamentalist who kills Gypsies and advocates genocide on them, tries to drown deformed babies, as well as lusting after a Gypsy girl named Esmerelda, and declaring that he will burn down all of Paris to find her. He burned down half of Paris, for the record. Through it all, he thought of himself as a Knight Templar who was never wrong, and convinced himself that it's Never My Fault about anything. There were a couple points when he might have realized that what he was doing was wrong, but each point became an Ignored Epiphany in the end. That's insane for you.
King Haggard: ...They are MINE! They belong to ME! The Red Bull gathered them one-by-one and I bade him drive each one into the sea!... I like to watch them. They fill me with joy. The first time I felt it, I thought I was going to die. I said to the Red Bull, "I must have them! I must have all of them, all there are! For nothing makes me happy but their shining, and their grace." So, the Red Bull caught them. Each time I see the unicorns — MY unicorns — it is like that morning in the woods, and I feel young, in spite of myself!
In Rock and Rule, Skip is unaware that he's working for the bad guys until a baby show explains the difference between good and evil to him. Mok may also count with his moral relativism mindset.
While Sid of Toy Story is a mean little brat, he does not understand that the toys he loves to mutilate and destroy are alive. As far as he can tell, he's just playing games. Or, to take it further, blowing off steam on "inanimate" effigies instead of actual living things. Except for when he stole his little sister's doll, ripped its head off, and screwed on the head of a toy pterodactyl on it just to laugh as he watches her cry.
The chef of The Little Mermaid. He just loves (maybe a little to much) to cook fish. Not knowing they were actually sentient.
Film — Live-Action
HAL 9000 from 2001: A Space Odyssey. While not directly explained in Kubrick's movie, the novel and sequel elaborate that he was programmed to be both completely truthful and keep the crew from the motivations behind the flight to Jupiter — and when the crew becomes inquisitive, he has to find a way to fulfill both. 2010 shows that HAL is not inherently ill-willed — he agrees to let himself be destroyed with the Discovery to save the Leonov's crew.
The title character of The Bad Seed puts the "Enfant" in Enfant Terrible, acting like a normal girl whenever she's not killing people. She's not sadistic in the least, and one character compares her Lack of Empathy to a blind girl not understanding the concept of sight. Some of her conversations with her mother indicate that she can't even predict how someone with empathy would respond to murder. This most emphatically does not make her any less creepy.
Nurse Ratched, the dictatorial head nurse from One Flew Over The Cuckoo's Nest, is likely genuinely trying to help her patients and improve society. Or it has to do with her being corrupted by power and/or simply being a sadist. Possibly also an example of an Unreliable Narrator, which was much more clear in the book.
Pain and Gain: Adrian and Daniel are so stupid that they seem to be totally unaware that they have done several horrible things over the course of the movie. Paul is just about as stupid, but he eventually grew a conscience.
In River's freak-out scene in Serenity, there is a brief moment where she is dancing gracefully through a willowy-white dream world... in her head. In actuality, she's dancing her fists and feet through anything that moves. She even Groin Attacks Jayne, even though he's trying to talk her down.
The various genocidal members of the Hutu tribe in Shooting Dogs seem to think they're doing the right thing, or are, at worst, a Necessary Evil.
V'Ger in Star Trek: The Motion Picture and the alien probe in Star Trek IV: The Voyage Home almost extinguish all life on Earth, both completely unaware that they are about to kill sentient beings. V'Ger actually does kill a lot of people, including some Klingons, the crew of Epsilon Nine, and Ilia, before realizing that they're lifeforms.
Bison himself doesn't seem to understand why people consider him a villain, even though he has a chandelier made out of human bones.
Practically every dinosaur in the Jurassic Park franchise. What, did you think T. Rex knew she was harming people by eating them? She was just hungry! Did the Dilophosaurus realize it was wrong to blind and maul Nedry? Of course not, it was hungry and curious! Did the Pteranodon stop to question how morally sound it was for her to snatch up Eric Kirby? No, because she was too busy thinking about what a tasty take-out meal he'd be for her kids! The only real aversions would probably be the Raptors and the Spinosaurus, who take almost sadistic glee in killing and eating people.
The Howlers don't know that they are massacring peaceful species in horrendous ways: it's all just a game to them and they actually have a playful disposition.
Dolphins are depicted similarly (and, in fact, the Howler mindset is directly compared to theirs), which means that this trope applies to them as well (at least in the Animorphs universe). This is Truth in Television, probably, as dolphins have been observed killing porpoises for fun. And orcas were once filmed killing a blue whale and leaving it to die without eating any of it at all.
The humans in Charlotte's Web. They see killing spring pigs at Christmas as perfectly normal. They never realise that they're causing Wilbur to feel much fear and stress when he is told what they're going to do to him.
The hadals from Jeff Long's The Descent may be like this, though not much insight is offered into their mental life. They are portrayed, to some extent, as almost sympathetically dumb and not terribly malicious, and yet they are fond of inflicting gruesome, senseless violence for no reason. It seems to be a product of their living environment, the deep, world-encompassing caves that cause peculiar Lamarckian mutations to their inhabitants; humans who colonize these areas quickly either die or assume aspects of the Hadal way of life, including casual cannibalism and sadism towards outsiders. The Hadals have been known to initiate surface humans to their society as a gesture of goodwill, or to replenish their numbers — this involves months of gruesome mutilation and rape.
Elves in Lords and Ladies. They torture and kill because it's fun. They have no understanding of what right and wrong are and possess no empathy, so their idea of what is good equates to whatever amuses them.
The assassin Jonathan Teatime from Hogfather does not seem to entirely understand that his actions (and he himself) are evil. As Susan Sto-Helit says when confronting him, "You were the little boy who didn't know the difference between throwing a stone at a cat and setting a cat on fire." Teatime is only an apprentice assassin. Not because he can't perform well, but because he is known within the Assasssin's Guild for lack of elegance on his assignments, which, in his case, means not only killing the target but nailing the target's head to the wall and killing his family, servants, and household pets on the way out for fun. Oddly enough, he actually likes animals—he just doesn't think of drugging a guard dog instead of nailing it to the ceiling.
In The Divine Comedy, it is this quality which separates those who can be redeemed (and therefore go on to Purgatory) and those who are damned (and thus consigned to Hell). As one angel notes, even a single tear of remorse is enough to allow someone to redeem themselves, no matter how twisted they are... but there are a lot of souls in Hell anyway.
The Buggers. They had no idea that they were killing actual intelligences since the average bugger is little more than an appendage. In their eyes, it was a war with no body count akin to a chess game until humanity took it a step further and killed their queen. The shock of this led the Buggers to finally figure it out and stop attacking, but then it was too late because humanity was traveling to their homeworld for revenge.
Well, Ender, too. After all, He didn't know all those simulations were real. In fact, he only blew up the Bugger homeworld because he believed that the higher-ups would never put him in charge of actual ships if they thought he would actually go to such extremes.
And in the sequel book Speaker for the Dead, the pequeninos ritually sacrifice several humans because it's how these aliens metamorphosize into their next form as sentient trees. Unfortunately, humans don't have a "third life".
Particularly chilling in The Giver. Jonas watches his own father commit infanticide, completely and blissfully unaware of what he's doing. The townspeople have no concept of death, and therefore, no idea that being "released" actually means being murdered.
According to some interpretations, the Eldritch Abominations that pervade the work of H.P. Lovecraft are Obliviously Evil. Many of them are not deliberately evil. They just don't care or don't even notice humans.
The gentleman with the thistle-down hair in Jonathan Strange & Mr Norrell is very much like this, stealing away people into Faerie in the belief that they'd be happier there, scheming to kill the magicians under the belief of their wickedness while speaking happily of massacring children, and making the life of his unwilling "good friend" Stephen Black a torment. As Stephen kills him, he admits that the gentleman only meant to help him, and apologises while dealing the final blow. In this case the strife is largely attributable to Blue and Orange Morality.
Robert Neville of the novel I Am Legend and its various adaptations is the last man in a post-apocalyptic world. He spends his time killing the vampire/zombie-like creatures that everyone else has become, thinking them mindless beasts. He later finds out that many of the infected humans had found ways to retain their sentience and he had been killing innocent people.
The interviewer scatters you all over creation, but he does not conceive that you can look upon that as a disadvantage. People who blame a cyclone, do it because they do not reflect that compact masses are not a cyclone's idea of symmetry. People who find fault with the interviewer, do it because they do not reflect that he is but a cyclone, after all, though disguised in the image of God, like the rest of us; that he is not conscious of harm even when he is dusting a continent with your remains, but only thinks he is making things pleasant for you; and that therefore the just way to judge him is by his intentions, not his works.
Barry, the vicar-turned-demigod in Mogworld, genuinely believes that God wants him to "purify" the world by destroying entire towns, brutally murdering and torturing people, and enslaving all of humanity. It doesn't help that God (well... a god) actually did tell him to do this and gave him the power to accomplish it.
In Isaac Asimov's The Naked Sun, it's revealed that a Three-Laws Compliant robot can be this. Though the First Law of Robotics is "A robot may not injure a human being or, through inaction, allow a human being to come to harm," Elijah finds that the Law is more accurately stated as "A robot may not knowingly injure a human being or, through inaction, knowingly allow a human being to come to harm." This comes into play when the murderer tries to create warships controlled exclusively by robot brains, making them more efficient and eliminating the need for a human crew. Any such warship would naturally assume that other warships would also lack human crews, allowing them to attack other warships without violating the First Law and allowing conquest of the galaxy.
October Daye: April in the novel A Local Habitation. As an uploaded intelligence, and of a childlike Dryad at that, she helps in murderous experiments because she doesn't realize that once someone is "offline" they can't be "rebooted".
The Michael Flynn story The Promise of God takes place in a setting where using magic erodes away a person's moral sense, so every magic user has to have a chaperone to constantly ride herd on them and stop them from, say, solving people's problems by simply killing them.
The "Chid" in Barrington J. Bailey's short story "Sporting with the Chid" are completely incomprehensible to humans. They're also instinctive surgeons with amazing biological engineering abilities, and when a trio of small time crooks ask the Chid for help, the results are appropriately horrifying.
The Aesop from the second book of Sword of Truth is "sometimes the greatest harm can result from the best intentions", which seems to fit. Also, Emperor Jagang seems to believe that he's on the side of good despite being an obvious villain. Given the Knight Templar attitude of Richard in the sequels, this sounds like a Broken Aesop...
Humans in Watership Down; keeping pests out of your garden and plowing up the ground for a new subdivision become the acts of evil gods.
Galadedrid Trakand of The Wheel of Time series has moments of this. He always does what is right, no matter who it hurts, even himself, even those he cares about, and he expects those hurt to understand why he had to hurt them. When he is confronted by two things that are opposed, but equally right (arresting his sister Elayne and her friend for being magic-users in the militant church's country vs. helping them get to a place of safety), his sister comments that this is the first time he's ever encountered this sort of situation, and she didn't know how he would act. Later (once they're no longer breaking the law by being in the wrong country), Elayne and her friend encounter Galad again, and ask him for help in getting to safety. He ends up causing a riot that basically turns into a civil war in order to procure a ship for Elayne and her friend. Because that was the right thing to do.
Galad and his men were on one side of the civil war. On the other side were the Dragonsworn, who thought it was the right thing to do to go around trying to convert everyone to Rand's cause, and then burning down their houses, towns, and fields when they refused. And the Dragonsworn were the other people that Elayne and Co. went to asking for help. The girls literally started a civil war on accident just for asking for help.
In The Long Earth, First Person Singular is a gigantic organism that was born on an alternative Earth as a single organism filling an ocean. When she found out about other individuals coming in from other worlds, she realised her own loneliness and set out to assimilate every organism in all the worlds into herself. Though she's incredibly intelligent, she doesn't view this as a bad thing, but the other organisms are inclined to take a different view.
In Germinal, the mine owners are a family of perfectly lovely people. Who are building their fortune on the backs of exploited miners working in horrible conditions and abject poverty.
This is sort of the modus operandi of The Addams Family, who are genuinely nice people — who just happen to not quite realize that no-one else shares their quasi-immortality, or finds torture, explosions, and other such morbid pastimes amusing. Of course, no-one ever bothers to even mention the fact that they are rather more fragile than the Addamses.
In the original comics, the Addamses seemed to have a vague idea that other people weren't like them, but didn't fully understand it — such as Morticia giving a babysitter/nanny the "friendly advice" that she should keep her back to the wall at all times while working.
On Angel, a demon is getting married to Doyle's ex-wife. As part of their culture, he must eat the brain of his wife's last husband to ensure a proper marriage. They are genuinely shocked and offended when Doyle refuses.
One of the killers in Criminal Minds was hallucinating that he was in a war zone and that his victims were members of the opposing army. In actuality, he was running around construction sites and his victims were innocent bystanders. In fact, a number of killers fit this trope by virtue of being insane or mentally disabled. Another good example is one murderer who committed all his crimes while in a state of psychosis, then couldn't remember them afterwards. He was absolutely horrified when he found out what he'd done.
On Gilligan's Island, the castaways are menaced by a gorilla who found an old cache of military weapons. The Professor realizes that the gorilla doesn't want to harm them. The gorilla was a witness to war and assumed that fighting was how humans played with one another.
This is one of the most chilling aspects of The Sarah Connor Chronicles. Cameron has a tendency to execute people or leave them to die when she has no further use for them, because her internal logic prioritizes her mission to protect John Connor above all else. In a few instances, she outright executes people whose only crime was to potentially endanger John's life; for example, she kills a trio of burglars who robbed the Connors' house because they had accessed their identification and financial information, but that information would allow someone else to track them down.
Interestingly, it's often proven after the fact that Cameron made the right call. For example, Sarah is horrified when Cameron kills Enrique just because he might have been an informant, but a message left on Ellison's answering machine reveals that he was indeed an informant, and he was about to reveal the Connors' location to the FBI. And in the case of the burglars mentioned above, the one burglar that Sarah let live (without Cameron's knowledge) ended up leading Cromartie to them.
The Borg from the Star Trek series have killed and performed Body Horror on countless species throughout the multiverse. From their perspective, conquering then modifying entities to become part of their Hive Mind is a great act of kindness. Scary thing is, those who have experienced this agree being part of a greater whole is quite joyous. They only object to forcing people to join.
An entire episode of The Next Generation is devoted to this trope, in the form of the Crystalline creature that destroyed Data's homeworld.
Maryann Forrester of True Blood. She uses her supernatural powers to control people's minds and bring a Zombie Apocalypse upon Bon Temps, and she ritualistically rends her victims and eats their hearts; she doesn't see what the problem is, and she does it not to be evil, but because she sees it as doing an honor to her god.
Danny, the alien collaborator from the TV series V, is pretty much this trope. But oh boy does it set him up for a Karmic Death.
An argument can be made for Rilane of Evillious Chronicles embodying this trope. Her lines in Daughter of Evil suggest that she might have had no idea that what she was doing was hurting people (possible, considering how she had pretty much been given whatever she wanted for her entire life and presumably had not been taught empathy for others), and she obviously regretted her actions in Regret Message and Daughter of White.
In GURPS Aliens, there's a hivemind called Mmm. It is all life on its home planet. Depending on where in the timeline you are... Mmm is either an Eldritch Abomination casually slaughtering humans, or an innocent pacifist playable character. And no, it isn't that it starts out innocent and then become evil. The murderous phase comes first, before it comes to the Heel Realization that humans are individuals and that individual human lives are irreplacable, and thus have value. It was innocently slaughtering people because it was curious about what they looked like on the inside and thought that mankind wouldn't mind losing a few drones.
Exalted is full of Knight Templars and Blue and Orange Morality, so some of this trope is to be expected. The best examples are the Solar Exalted of the First age - who were often so disconnected from humanity and completely assured in their own righteousness that they never actually stopped to consider that maybe they could be doing more harm than good - and the Fair Folk - who come from the chaotic Wyld outside of Creation, and sometimes have trouble with human concepts like "death is permanent."
Some followers/demons of Nurgle are very happy and just want to hug others and make them a part of the family of grandfather Nurgle. They don't get why being rotting zombies with gaping weeping sores (among other things) isn't desirable to others. Nurgle is, quite literally, likened to a jovial grandfather. He's easily the nicest of the Chaos gods.
This side of Nurgle is emphasized by his daemonic beasts, giant plague-ridden, acid-oozing slug-creatures called the Beasts of Nurgle; they're killing machines with the minds of playful, friendly puppies, who don't realise why their "playmates" become so dull and silent after a short hug. One of the more recent additions to the daemonic arsenal is the Rot Fly; the grown up form a Beast of Nurgle assumes once its perpetual bafflement gives way to resentment of the way that mortals won't play with them, becoming malevolent, flesh-eating fly-monsters.
Then there's the arguable case of the Thousand Sons, who received so many "gifts" from their patron god Tzeentch that they were beginning to turn from gene-boosted human sorcerers to gibbering monstrosities. Arguable because whilst the denizens of the Warp often appear genuinely clueless about the limitations of the mortal physique, assuming that Tzeentch acts out of ignorance is seldom a wise move.
There's also the Orks, who fight, maim, and kill their way across the universe because... it's fun. And it's what they were made to do. And all the other Orks are doing it. And it just feels right. They also have absolutely no fear of death, and consider a good enemy who can provide a hard fight to be a resource worth cultivating and releasing if captured; it's as close as they come to the idea of a friend.
This is apparently standard attitude for the Imperium, as in one Last Chancers novel one of the title Penal Legion actually thinks that xenophobia towards humans isn't a very good reason for wanting to start a fight with a human, apparently forgetting the fact that the Imperium pillages and slaughters any alien species they come across, more often than not pursuing the race to extinction or very close to it.
Averted in Dungeons & Dragons. Any creature that doesn't have the capacity to comprehend good and evil (those of animal intelligence, that is) are always neutral, no matter how much destruction they cause. This includes the tarrasque, which is capable of mass destruction when it's active.
It is still entirely possible for this to be played straight through means other than just being too unintelligent to comprehend good and evil, of course. And there is one exception to the animal intelligence rule (or rather, another rule that supersedes that one) — beings who are at least partly made of an alignment have that alignment as a default even if they have animal intelligence or are even mindless.
Marauders in Mage: The Ascension are crazy mages whose powers constantly (and unconsciously) reshapes reality around them to follow their delusions. As the nature of their madness is such that they can't ever understand that they are living in their own alternate reality, they often cause an incredible amount of chaos and destruction while acting (from their own perspective) in a sensible and rational way.
Martha and Abby in Arsenic and Old Lace are two charming old ladies who invite charming old gentlemen to tea, then bury them in the basement. They haven't the slightest inkling there's anything wrong with their serial poisonings.
Ignus of Planescape: Torment, a longtime Pyro Maniac, whose mind has been too scrambled by being turned into a conduit to the elemental plane of fire to realize that other people might take issue with his desire to set everything on fire. After all, being able to be on fire 24/7 was the best thing that ever happened to him, how could anyone else object to that?
In Immortal Defense, you're introduced to a group of quirky and lovable Points that represent your emotions, which you use to fight enemies. And they go on being quirky and lovable while you use them to commit genocide, betray a people who worshipped you, and kill millions of relatively innocent aliens while defending — BIG FREAKING SPOILER: — a rock in space that you've deluded yourself is your dead homeworld come back to life.
According to the trophy files, Super Smash Bros.' Mr. Game and Watch has no concept of morality or good or evil, hence him doing what the bad guys wanted for a while.
Shadow of the Colossus is a case of this, but then again, there is never any doubt that the Colossi would leave you (and the rest of the world) alone. You are the one going into their lairs and stabbing them in the head or armpit because of a deal with an ancient, morally ambiguous entity.
Taro Namatame represents what the protagonist might have become had he jumped to conclusions about the Midnight Channel and the TV World that lead him to kidnapping people and abandoning them in a parallel world for their own safety. Not unsympathetic, as he is an Unwitting Pawn who eventually repents when shown that his attempts to help people actually endangered them. A tragically terminated relationship followed by heavy substance abuse might help explain his lapses in judgement, as well.
Subverted with GLaDOS, who at first seems to be malfunctioning, trying to maintain its original purpose while the tests have become a Death Course due to lack of maintenance. When you go off-track and destroy the first Personality Core, she reveals that she knows exactly what she's doing.
On the other hand, Aperture's founder Cave Johnson fit this trope like a glove. At first he saw himself as a brave entrepreneur, doing slightly questionable experiments For Science!! Then when he started to fall ill, he named his beloved secretary as the head of the company — whether she wanted it or not. He didn't seem to realise that she was terrified of the Brain Uploading process, or that the body he was putting Caroline into would turn her into the evil GLaDOS.
The shibito (literally "corpse people") in Siren fit this trope precisely. They seem like zombies, walking around with fatal wounds, but their motions resemble that of a marionette on invisible and intangible strings, they speak with a reverb in their voices, go about twisted parodies of their living existance, and they seem genuinely happy with their condition. They wish to spread this "happiness" to others, attempting to cheerfully slaughter any living person they can find.
System Shock 2: not Shodan, she's consciously hostile, but The Many. They invite you to join their Hive Mind as if that should be the most attractive invitation, oblivious to the insanity the Body Horror of "joining" them has driven other humans into. A milder version would be the android assistant who attentively and helpfully approaches like a homing missile on legs.
Knight Commander Meredith, the leader of the templars, has been corrupted by a bizarre artifact made of lyrium, a magical ore that has some strange side effects, causing her to give the templars an order to kill all of the mages.. It's not clear how much the idol is affecting her, but in the final boss battle, it clearly is.
Merrill from the same game could also qualify. She's hopelessly naive about the dark magic she casts, to the point where any of her actions that result in somebody's death (and, even on her best possible campaign, that's still a lot) come as a complete shock to her. The deaths are generally not directly her fault, but more a matter of people reacting in a panic based on their own expectations of her and thus getting themselves killed... which meant she could keep believing that she wasn't doing anything wrong.
Pokémon Black and White: Up until the very end of the game, N honestly believed that all Pokemon were inevitably abused by trainers and that the only humane solution was to separate them. When he finds out that not only was the entire Team Plasma operation a front for Ghetsis to get rid of any competition, but also that his entire worldview was deliberately misshapen and manipulated by Ghetsis and that he'd been wrong the entire time, he was... distressed, to say the least. An interesting thing to note about N is that he was acknowledged as a hero by one of the two major legendary Pokémon of this generation. N was the hero of ideals while the player character, acknowledged by the other legendary, was the hero of truth. Also, unlike the player, who had to battle the legendary who sided with them, N simply befriended his legendary, like he did with every other Pokémon he fought with throughout the game. Another thing to note about N is that he didn't try to separate everyone from their Pokémon by force; he wanted them to recognize him as the hero of legend and willingly release their Pokémon. Sadly for him, however, a Plasma scientist that hacked into the storage system was preparing to release everyone's Pokémon regardless...
There's also Archie and Maxie, the villains from Pokémon Ruby and Sapphire, who truly believe that it would be a great idea to flood the world or dry the oceans, respectively; admittedly, their original plans weren't quite that extreme, and once they realize that that's what they're doing, they both pull Heel Face Turns.
Debilitas from Haunting Ground; he relentlessly stalks Fiona because he thinks that she's a new doll for him to play with, however, like Lennie from Of Mice and Men, his enthusiasm makes him dangerous to be around.
Thankfully he can be saved in a New Game+. Instead of killing him you instead drop a chandelier on him. That stuns him and than he looks at a statue of a goddess and then at Fiona and thinks she's the goddess. He gets a happy end in that after everything is over and done with he tends the garden of the mansion.
In Advance Wars: Days of Ruin, both of Caulder's/Stolos'Opposite-Sex Clone daughters, Penny/Lily and Tabitha/Larissa, arguably qualify as this. Penny is a small child whose mind is thoroughly broken from too many experiments and appears to think razing the landscape and blowing people up with tanks is just a fun game she plays with her family. Tabitha's older and crueler than Penny, but a good deal of her dialogue, (especially in the questionably-canon tactics segments) implies she doesn't really understand that testing her dear old dad's horrendous super-weapons in live combat on a rag-tag group of survivors just trying to live in peace is wrong.
In the EU translation Dark Conflict, Lily is still presented as Obliviously Evil but Larissa is not: she is a Social Darwinist and enjoys picking on the weak and blowing up things out of her own volition.
The Pyro from Team Fortress 2 is this. From his/her/its point of view, the battlefield is a Sugar Bowl in which he/she/it skips about, spraying rainbows and bubbles and giving candy to the happy and giggling opposing classes in baby cherub form. Actually, he/she/it stalks about searing people's flesh from their bones, ignoring their dying screams of agony and pleas for mercy as he/she/it hacks them apart with a fire axe. It is pictured at the top of this page, imagining himself spraying about a stream of rainbows when in reality, he/she/it is setting fire to the opposing team's base.
Edna & Harvey: Harvey’s New Eyes sets the stage early on, when Lilli inadvertently puts a fellow student in danger, and hears a scream. She returns to find the student "missing", but displays absolutely no interest in the motionless human-shaped lump nearby (which she perceives as covered in pink paint). As the game proceeds, that pink paint becomes a lot more common.
Handsome Jack from Borderlands 2 outright states that he is the hero of the story. What's worse, he believes that it's actually the player who suffers from this trope.
Possibly Kharla'ggen from Drowtales, since it's been hinted that she just doesn't have the mental capacity to understand what she's doing, and just wants to play with her dolls. And eat demons and consume their auras, the only thing that she proactively takes interest in as the theoretical ruler of her clan. Demons and dolls, those are the only real things to Kharla, or so it seems.
The skin lizards. They don't get why people are so intent on keeping their skin.
Values Dissonance plays a huge role in Digger. The hyenas practice funerary cannibalism, something which causes Digger some trouble (being a strict herbivore) and greatly confuses Shadowchild in its morality lessons (one of which had been "don't eat anything that talks"). After his Heroic Sacrifice, Digger allows the skins to take Ed's, because they had befriended him and meant to honor him by it.
Din and Jin from Las Lindas. They genuinely just want to have a good laugh at the other characters' expense, but their latest "prank" was not funny. At all.
In No Rest for the Wicked, the witch from Hansel and Gretel isn't eating children out of malice or hunger. She lived out in the woods with her children (named Hansel and Gretel) but they were slowly dying from sickness. Going mad with grief, she thought there was no place to keep her children safe... except "inside". When the townspeople started abandoning their children in the woods, she thought that the lost children were Hansel and Gretel, who "escaped", and took them 'back in' again.
Witch: You two just think it's a wonderful game don't you... always sneaking out somehow... pretending to be different children? Even if you look different everytime, you can't fool me. In the end, it's always the same.
It actually somewhat disturbing when Red is pushing her into the oven and the witch starts to scream that they can't do this, she has children and no-one else can care for them...
Depending on how the metaplot finally plays out, it's entirely possible that the PCs of Darths & Droids may end up, through simple carelessness and/or Genre Blindness, instigating or abetting each and every one of the evils that Star Wars Episode III ends with, including, but not limited to, the Galactic Empire, the Death Star, Boba Fett, and Darth Vader. So far, only Pete seems to realize this, but he's in it For the Evulz anyway. Annie is also pretty clear on what she's doing, having intentionally written Anakin to be slightly unhinged and on the edge of sociopathy.
The Angelo's Kids religion from Our Little Adventure. They seem genuinely happy to carry out Angelo's wishes. They destroy entire towns, kill entire populaces, and pillage and loot, all because they believe in Angelo's vision of a perfect world. Though some of them aren't so blind about it (notably Umbria) and still do it out of genuine sadism or racism.
Characterization Marches On makes it hard to say where the title character of Niels falls on the morality scale, but if this is any indication, he's certain that any good people he kills will be rewarded in heaven.
Miko. She genuinely believed herself to be personally chosen by the gods to accomplish some great task and therefore everything she does is their will made manifest, and will not let anything, even the revocation of favor from those same gods as a sign that maybe she wasn't.
It's hard to say for certain that Kornada in Freefall is this, but at no point has he ever acknowledged or even appeared to consider how much harm his actions have caused. He simply wants more money, and he'll do whatever it takes to get that money, whether it's firing someone so he can retroactively blame them for sabotage if things go wrong, or leaving someone to drown rather than taking the time to save her, or destroying the minds of millions of robots as part of a plan to steal their funds. It's not that he's good, either — he's never done anything to help someone that hasn't benefited him — but the concept of good and evil seems above his capacity to comprehend. The only distinctions he makes are fair and unfair, and it's only unfair if someone else has something he doesn't.
Kornada's personal assistant is a robot who literally cannot comprehend that Kornada's best interests are not anyone else's best interests, and tirelessly pushes for the aforementioned robot mass mind-erasure with the belief that it's doing good.
True Villains: Mia, who seems to be this way. So far, she's built a massively powerful golem that stomps another one that had so far survived Elia's undead army and a potion that had previously been shown to blow up an entire town (!), helped Bayn steal Lord Attera's valuables to get his attention and played an important part in getting rid of The Paladin after Elia and Cecil fail to do so alone.And she's as carefree and cheery as ever.
Tangerine/Pebbles of Sinfest steals and threatens people with fire and katanas and does it all in apparent unawareness that she's doing anything wrong. Likewise Absinthe seems to make no connection between the souls she purchases and the ones in the fiery pit.
Venus the Living Swamp in the Skin Horse storyline "Come Swing From My Branches" is obsessed with her lost love and oblivious to any suffering her vengeance might cause to innocent people. When she returns in "My Brother Sam is Dead", she's mostly acting out of hunger. This leads to a dichotomy in Unity's mind: Smart!Unity thinks Venus still needs to die for the safety of others (and also revenge for the events of "Swing From My Branches); Regular!Unity feels this would be killing an innocent, and it's not like rampaging bioweapons that eat people can't be good, because she's one.
The SCP Foundation brings us the Plague Doctor known as SCP-049, whose touch kills people, allowing him to preform a surgery that turns them into homicidal zombies known as SCP-049-1. When he once spoke to a SCP doctor he explained that he was curing them. Of what exactly isn't clear, but apparently few of the people who work at the foundation have it.
This trope was applied when The Simpsons' Montgomery Burns lost his fortune and Lisa convinced him to be "environmentally friendly". He honestly tried to do the right thing, but.... "What's wrong with Li'l Lisa's Slurry? It's made of 100% recycled sea animal!"
Lisa: You're still evil! And when you try to be good you become even MORE evil!
The oft-mentioned-on-the-trope-page Alternate Character Interpretation of Rusty Venture in The Venture Bros. is that he is actually more of a villain than a hero. At one point, he asked Brock if he was a bad person. He seemed genuinely upset at the concept. It also doesn't help that Brock is reluctant to say he's evil. He doesn't think Rusty's evil, he just thinks he's a Jerkass. And he's right.
The Ice King seems to fall under this. He kidnaps countless women because he wants nothing more than to marry a princess. Later, he actually steals body parts from his favorite princesses and makes them into a princess for himself. He treats his Princess Monster Wife like a sweetheart, oblivious that he has committed a hideous crime.
Lemongrab. He thinks that he's doing a good job ruling the kingdom, and his intentions of order and quietness are fair enough, but he makes all of his subjects miserable by sending them all to the dungeon. He isn't evil, though — he's dysfunctional and unadjusted to living, socially inept, and an idiot. Later episodes change this dynamic a bit, to the point where the question of how responsible for his actions he is make him more than a bit of a Base Breaker.
Ozai: There is no right or wrong apart from what you decide. Who you choose to defend deserves to be defended simply because you chose them. You are the Fire Lord. What you choose, by definition, is right''.
Baljeet in the Phineas and Ferb episode "Cranius Maximus". He's not trying to kill all life on Earth by eliminating the atmosphere, he's just been driven partially insane by his newly-enhanced intelligence, and figures it's the easiest way to see the universe better.
Cartman: I'm making the world a better place, Kenny! Kenny: For you! You're making the world a better place for you! Cartman:(beat) Right, that's what superheroes do.
Later episodes of Sponge Bob Square Pants seem to have the title character, Patrick and Mr. Krabs as this; SpongeBob doesn't mean to hurt or annoy Squidward or drive him insane, all he wants is to make him happy and have fun. Patrick's just too stupid to know any better. Mr. Krabs, while usually just flat-out evil, does genuinely seem to believe that his greed helps his business. Best illustrated in "The Krabby Kronicles" when he responds to SpongeBob's concern about their tabloid newspaper:
Mr. Krabs: How many times do I have to tell you, boy? We're not hurting anyone!
In the My Little Pony: Friendship Is Magic episode, "A Friend In Deed", Pinkie is just trying to make friends with Cranky Doodle. Unfortunately, this involves publicly humiliating him, stalking him, breaking into his home, accidentally destroying his most prized possession, and otherwise terrorizing him.
And in "Too Many Pinkie Pies", her mirror pool clones just want to have fun!note Fun! Fun! Fun! Fun! Ooh! A TV Tropes page! That looks fun!
"Wonderbolt Academy" gives us Lightning Dust, a hotshot who seems to believe that her need to prove herself and score points in exercises comes above the accomplishments and physical wellbeing of other ponies, to the point that her response to nearly killing five bystanders is "Yeah, so?"
The Adventures of the Galaxy Rangers had a couple cases, mostly with their Green Aesop episodes. In "Space Moby," the whales didn't understand that their asteroid feeding endangered the miners and the Honest Corporate Executive that wanted the whales destroyed was just trying to protect his employees. A compromise is reached, and everyone wins. And in "Progress," the pair of aliens who set up a factory on a remote world didn't realize their "progress" was causing damage to the environment and driving the ocean-swelling inhabitants insane. They figure out how to turn a profit making pollution cleanup machines instead.