Arc Rise Fantasia gives us Eesa. There doesn't seem to be any real reason why she shouldn't help bring about L'Arc's Law to save the world since she makes it clear that she only wants to choose the Laws that are best for everyone, yet she's still the final boss. Umwat?
Borderlands 3 has Killavolt, real name Kenneth, a former husband of Moxxi who drank battery acid after the divorce and became a bandit chief. Besides working for the Children Of the Vault, being a bit of a jerk, having a small penis, and being bad at sex (the latter of which the player is reminded of ad nauseam), he doesn’t really do anything evil. He doesn’t recruit people like Mouthpiece, supply guns and vehicles, or even plan operations. He just sits there in Lectra City, watching a battle royale where the winner gets to sleep with him (which Moxxi demeans the contestants for). It gets even worse when you realise that by killing him, there are more COV members running around and doing things to actually advance Troy and Tyreen’s goals rather than watching his battle royale and killing each other. At that point, Moxxi’s hiring the Vault Hunters to kill him is solely out of spite.
Dissidia Duodecim reveals through Chaos' backstory that he really isn't evil at all—he's just doing what Garland, Cid, Cosmos, and Shinryu have told him to do and as such, this is an Invoked Trope. It just happens he looks like a monstrous demon, and most of the warriors he calls to serve him are villainous.
Touhou Seirensen ~ Undefined Fantastic Object offers a rare encounter: in one route, at least, Marisa and Byakuren seem to hit it off on the subject of magic use, end-up sidelined by a painfully short theological disconnect ("'youkai' protected from humans" versus "humans protected from 'youkai'"), and it's the last boss who demands the fight. Marisa might have been rude (as always) but Byakuren didn't even try hard.
Played with, where the heroes assume that Gulcasa and his army must be evil because they conquered Fantasinia and killed King Ordene. They eventually realize — while invading Gulcasa's country — that they are wrong, but continue their invasion (and in doing so, wipe out a third of Bronquia's able-bodied population in this campaign alone) because they think it's too late to turn back. The Royal Army spends the rest of this part of the game slaughtering civilian militias and the remnants of the Imperial Army, who insist that protagonist, Yggdra, will have to go through them if she wants to kill Gulcasa. There's also some vague nonsense about Bronquia trying to bring about The End of the World as We Know It by resurrecting an ancient demon, but from the way Gulcasa and his last few generals talk about this planned resurrection, it was actually supposed to be their very last resort in case Fantasinia retaliated by invading them. Welp.
The game, given its tendency to use Grey-and-Gray Morality, uses this in-universe quite well with Big BadDr. M. He's fighting off the Cooper gang and is held at gunpoint by Inspector Carmelita for it. He points out that since he legally owns the island where the treasure is (and by extension, the treasure hidden there), he is simply defending himself and his property from a group of wanted, notorious criminals who are attacking his home, henchmen, and trashing the place.
M also plays the trope straight. The reason Sly goes up against him is to get his hands on a huge amount of gold and treasure that M is trying to steal. Sly claims the treasure belongs to him since it was amassed by Sly's ancestors. The problem with that claim is that nearly all of the treasure was obtained through theft, so Sly has just as much right to it as M does - which is to say none at all. Even Sly's claim that he's entitled to it because it belonged to his father is contestable as Dr. M was his father's teammate and thus has some stake in the treasure as he helped the father earn it to begin with.
And just to make things even more complicated, while Dr. M's primary goals and motivations are, as stated above, neutral-to-legitimate, he's still clearly a villain, considering he poisoned one of his lackeys (who he knows full well has a wife and son) for incompetence, attempted to murder an Interpol agent, and continued to attack even as Sly tried to retreat.
Daleth from Shin Megami Tensei II is a literal example. He was created by the Center to be the anti-Messiah so the main character can defeat him and grow more popular. Ironically, he's one of the few named characters, aside from the protagonist and Hiroko, to have a happy ending. He even gets a pretty girl who loves him dearly. Beth, Gimmel and potentially Zayin, all intended to be heroes, end up dead.
Most of the Portrait Ghosts in Luigi's Mansion don't even attack, and seem fairly content with just hanging around the mansion. Keep in mind Luigi isn't a Designated Hero, he's just making sure all the ghosts are captured and some of them happen to be the said villains.
While this is debatable, in BlazBlue, the NOL is straddling this line. For the most part, the organization is filled with lots and lots of Punch Clock Villains, who were doing their jobs for their paycheck, and they truly believed in their goal in creating a peaceful world free of conflicts. However, because Ragna mainly opposes them and they employ several villains like Hazama and Relius, combined with the fact that they are mainly composed of rich people and make up some dictatorship rule (even if it's for preventing total chaos), it becomes easy to paint them as a tyrannical group of villains or a merciless Empire type organization.
Cao Cao and the Wei forces in Dynasty Warriors, in keeping with his characterization from Romance of the Three Kingdoms. In fact, the game runs on this. No matter who you play as, the other 2 kingdoms (and minor forces) tend to be painted as the bad guys - which makes sense since they're trying to unite China under their rule too, so it's a conflict of interest. The exceptions are Dong Zhuo and, to a lesser extent, Lu Bu.
Played with in Star Ocean: Till the End of Time. During the search for Amelia, you run into Rodger and then run into a bandit leader. He was willing to ignore you and go about his way, but the party members kept saying he looked 'evil'. The only reason you fight him is because they wouldn't stop saying that and the bandit snapped.
In X3: Albion Prelude, the Terrans are evil for demanding justice for a terrorist committing an act of genocide that appears at first to be conducted purely out of racism. To be more specific, as far as you can tell in the game, the cause of the Second Terraformer War between the Terrans and Argon Federation is that Saya Kho suicide-bombed the Torus Aeternal (massive space station ringing Earth's equator) for little reason, an act that killed thousands of Terran civilians and military personnel instantly, then millions more from deorbiting debris.
In a rather extreme case of All There in the Manual, the war started because the Terran intelligence services were infiltrating the Community of Planets with the hope of influencing its future course, due largely to the Terrans' paranoia about artificial general intelligence. This ended up as a Self-Fulfilling Prophecy: the Argon began working on AGI combat vessels in order to give their military a fighting chance against the Terrans' technological superiority, then used them to invade the Solar System in a preemptive strike when they discovered the Terrans' spy network. Saya Kho infiltrated Sol as an agent of the Argon Secret Service; her attack on the Torus was intended to open the way for an Argon invasion of Earth. So, while a little more nuanced than it originally appears, there's still the fact that the Argon struck first.
The Reapers in The World Ends with You, at least the ones outside the big four, and it's debatable. Really, they're just doing what they're supposed to do, and their erasing of players is actually important to keeping the universe in balance and humanity constantly evolving based on what we learn in secret reports. Also, while Minamimoto and Konishi are obviously villains, Yodai was simply doing his job and Kitaniji was trying to save the UG from complete destruction with an Assimilation Plot, although Neku and the player don't learn this until after Kitaniji has lost.
The Enclave in Fallout 3 can come across this way, especially to people unfamiliar with them from Fallout 2. True, they hijack Project Purity and their leader's plan is pretty horrific when you learn of it. But the subordinates of the Enclave seem more level headed in comparison and more interested in governing the Wasteland rather than destroying it. And considering the Wasteland is a pretty horrible place to live what with the wandering gangs, super mutants, and poor living conditions, and they have by far the most advanced technology available to enforce order albeit with brutal tactics, the player may find himself wishing there was an option to side with them rather than treating them as Always Chaotic Evil. It gets even more clear if you foil President Eden's plot, at which point the Enclave's plan is simply to turn on the water purifier - something everyone wants to do anyway. Notably, by the time Fallout 76 rolled (well, fumbled) out the gate, the Enclave are a joinable faction.
Canach as the villain in the Secret of Southsun and Last Stand at Southsun arcs. After accidentally inciting some monsters to attack a major city, Canach is arrested, but claims to be a protector of the weak. He eventually disappears in order to sabotage the Consortium he used to work for. The player is ultimately tasked to stop him, which they do. The only problem is, long before you defeat him, you learn that the refugees that had settled the island had been tricked into virtual slavery thanks to the Consortium's contracts and Canach's goal was to end this injustice. Canach only fought the heroes in self-defense when they came after him, and the authorities had been refusing to help the settlers until Canach forced their hand. Ultimately, you fulfill his plan by destroying the odious contracts, but the game still acts like locking Canach up and throwing away the key is a just outcome. Why he was wrong and the heroes were right is never adequately explained.
The Ascalonian humans suffer a strange form of this retroactively. In the first Guild Wars campaign, you played an Ascalonian forced out of their homeland by the Always Chaotic Evil Charr. In order to make the Charr playable in Guild Wars 2, Arena.net took steps to Retcon their Always Chaotic Evil nature, partially by attempting to reframe the war as not a defensive one on the human's part, but a rightful reclamation of land on the Charr's part. In an attempt to make it more ambiguous, a new event was added to the lore after the player's left Ascalon, where the king who remained behind, surrounded by enemies, activated an ancient spell that succeeded in destroying the nearby Charr... but also cursed him and his people to forever wander as ghosts who still think they're fighting the war. This is treated as a Moral Event Horizon for the king and, by extension, the Ascalonians, by humans and Charr alike in the present. There are still two problems with this, however. First, that the king had no idea that would happen. Second, that from what we saw in Guild Wars, there was no indication that the humans knew the land used to be owned by the Charr, and the Charr's response was not diplomacy, but casting an apocalyptic spell that reduced the entire region to a barren wasteland for at least 250 years. Not only that, but the Charr who led the attack were from a faction that is recognized as evil to this day. Despite this, the Charr are treated as being completely justified for hating humans and it's treated as something humans should learn to put up with, while bitter, modern descendants of Ascalonians are treated as dangerous zealots.
Duke Crabtree from Zap Dramatic's Ambition. We're apparently supposed to see him as an egotistical jerkass who is out to steal your job, but he appears to be far more competent than the player character. He'd probably be better suited for the job. While we as the detective spend about half of Episode 6 sleeping, Duke is actually doing work. While interrogating Bridget, if you end the interrogation too early, Duke will helpfully inform the player that Bridget contradicted herself and tell us to go back and "nail her." When you are interrogating Bridget near Ted's cell, Duke will ask the valid question of why we are exposing the suspect to a known violent criminal. One possible response to this is to call Duke a meddling creep and then punch him in the face. This results in a game over, but the fact that the option is there in the first place clearly indicates that we're not supposed to like Duke. Duke does insult the player, but the attentive player should notice that Duke only insults you when you waste time, and after you get a confession from Bridget, he stops insulting you entirely and works with you to try and solve the case. Somewhat negated by the fact that Duke actually becomes genuinely villainous in Episode 10. It is revealed that he is in on the plot to frame Ted Hadrup for murder, and then he hijacks your cab and takes you somewhere to kill you. However, he still qualifies because we're supposed to see him as villainous from the start even though he doesn't do anything particularly villainous before being revealed as Evil All Along.
Helen is portrayed as unreasonable and overemotional about her husband cheating on her. In "The Tryst," telling Yale to break off his affair with Angie and stick with Helen causes you to lose. Yale then mocks you for thinking that having an affair is at all a bad idea, before throwing you out and saying that you have a limited future, unlike him, because having an affair means he has "ambition". Amusingly the narration set up that the Player Character is only talking her down not because she wants to club her husband with a violin but that the violin is a gift from his/her aunt and is too tired to call the cops.
To a lesser extent, Angie. Presumably the player is meant to share Ted's outrage that she would conclude that a man who threatened to blow up an office building and rambles on about getting his orders from God might just be a touch crazy.
Queen Odette from Odin Sphere acts cruel and sadistic most of the time and treats the living as inferior, but when it comes down to it, she just wants for everyone to stop breaking into the Netherworld to bring people back to life, and stealing her jewels to create Psyphers to kill more people while corrupting the natural flow of life. The only really villainous things she does revolve around Oswald and his Magically-Binding Contract with her (granted, he wasn't aware of the conditions when the contract was made, but that was because the contract was made by somebody else who didn't have his best interests at heart), and trying to murder Cornelius simply because he wants to leave the Netherworld after being hurled in there unconscious, against his will, and innocent of wrongdoing. In fact, when she's finally Killed Off for Real, King Gallon is able to take control of the Netherworld's forces and help trigger Armageddon.
The Mayor's wife in the second Skate or Die game is portrayed as overreacting in her quest to ban skateboarding even though you ran over her poodle with your board. (Icepick was involved, but still.) Worse, to change her mind you attack her with a paintball gun.
The Vaadwaur in Star Trek Online: Delta Rising. Yes, they're basically Space Nazis and their leader Gaul has no qualms about gunning down civilians in cold blood. But neither did the Romulans, Klingons, or Cardassians, and the Federation had a detente with them for decades. The Vaadwaur are also an endangered species who used Human Popsicles to escape extermination by an alliance fighting back against their imperialism. The real problem, though, is that their enemies the Kobali come off as the Designated Hero. While they're the Alpha Quadrant nations' ally against the Vaadwaur, the Kobali come off as Holier Than Thou with a Culture Justifies Anything attitude, and for all practical purposes contribute little of worth to The Alliance (their population is going to be fairly low for various reasons and their only modern warship was built with Alpha Quadrant technology). Plus, their method of reproduction, basically necromancy, has drawn many rape comparisons, especially given that they're holding several thousand Vaadwaur cryo tubes and using the failed ones for more stock, along with making use of Vaadwaur battlefield casualties. Gaul jumps off the slippery slope in "All that Glitters", but the storyline reveals that the Vaadwaur high command are all infested with Puppeteer Parasitesexcept for Gaul, suggesting they wouldn't have willingly gone along with his plans.
Sunry in Star Wars: Knights of the Old Republic was a Republicveteran who settled down on the Awesome Underwater World of Manaan following the Exar Kun War. When the Player Character arrives, they find that he's on trial for murdering his mistress and forced to serve as his attorney. Through investigation it's revealed that Sunry did do the crime, but only because he discovered that she was a Sith spy using him for information. The player's Karma Meter is only affected if they lie to the court, and the quest's Golden Ending has you get him off through the Sith's lack of evidence while convincing Manaan to sanction them, but the narrative itself presents Sunry as in the wrong (not just for cheating on his wife) as your Cool Old Guy companion Jolee who knew him personally regards him as a Fallen Hero and Carth gives him a "The Reason You Suck" Speech for killing an unarmed combatant. Worse, Dummied Out content shows that she was planning to kill him herself, making his actions completely justified (especially since she's a Force-sensitive and he's a weak old man), and even though he wasn't aware of that, had it been included, it likely would have made it even worse.
Tales of Destiny 2: While Elraine is definitely evil, albeit in a well-intentioned way, the goddess she serves, Fortuna, isn't shown doing anything evil at all until the very end, when she's rejected by the very being she created, and even helps the heroes return to the present at one point. In fact, she's trying to bring eternal happiness to the world. It's the lengths her Saint goes to to resurrect her (she needs prayer badly) that she may not even be aware of (her instructions to her Saints seem to have been pretty vague, along the lines of "find the best way for me to help humanity") really cause the heroes to oppose her presence. At worst, she herself had Blue-and-Orange Morality.
Valkyria Chronicles 4: Forseti who is actually Kai Schulen defected from the Atlantic Federation to the East Europan Imperial Alliance because the Federation was doing secret experiments on girls with Valkyria powers and using them to power their Snow Cruisers and Ragnite Implosion Bombs. While the Empire was also doing it's own experiments, Forseti's goal was only to stop the Alliance's and free the trapped girls. Despite this, the game treats him as if he has become pure evil, and he is shot by his sister Leena Schulen while trying to rescue Angelica from being used as a power source in your reactor. The game treats this as completely necessary, despite the fact that he was completely unarmed, limping with a cane, and surrounded by heavily armed soldiers. Meanwhile, the so-called heroes are trying to Use the girl's powers to destroy the imperial capital, killing 8 million people, mostly civilians, in the hopes that it will end the war.
Overwatch: Symmetra is working for the corrupt Vishkar corporation. She's in fact an altruistic, autistic person who wants to genuinely improve other people's lives instead of just in it for more profit, prefers not killing others and does doubt about whether Vishkar was really living up to their words that they are trying to make the world a better place, her worst crime is 'doing corporate espionage' on Vishkar's orders (compare with some who murder at their own will). But since the narrative designated Vishkar as one of the bad guys (the corrupt corporate type, and unlike Symmetra, they rightfully earned it) and the one who opposes them, Lucio, is genuinely good and friendly, averting the Designated Hero, and the new Overwatch saw him as the picture of a hero after his opposition, the narrative lumps Symmetra as a villain character with her company, while she is an Anti-Villain, sometimes the narrative and the fandom kind of like to omit the 'Anti' part, especially pre-nerf when Symmetra could completely destroy entire teams in Quick Play with impunity.
King Aelfred the Great in Assassin's Creed: Valhalla has been marketed as the antagonist of the game since he opposes the Viking invasions of England which are depicted as not just outright raids but simple migrations to escape the violence and chaos engulfing Scandinavia. This was actually a case of Misaimed Marketing as Aelfred in-game not only opposes the Order of the Ancients despite being a Grand Maegester but he has no problem working with Eivor to expel the last vestiges of the group from the Anglo-Saxon kingdoms of Britain. It was very much intentional by the developers to show that neither the Saxons nor Vikings are all that good or evil.
Final Fantasy Crystal Chronicles has Jack Moschet, the owner of Moschet Manor and its respective mrryh tree. While the game justifies its previous boss battles by having them stand guard over the myrrh tree you need to make use of, the level is instead spent actively hunting down and killing Jack's tonberry chefs to provoke him into a fight when there's no indication that you need to do so, as the tree is just outside the manor in a different area.
Persona Q2: New Cinema Labyrinth's movie labyrinths have some intentionallyreally dubious Designated Villains along with equally dubious Designated Heroes. Part of the mission for each level is doing some major script edits to a more sane moral code. If you notice a running theme in the movies, it's deliberate; the movies combined are, for all intents and purposes, OG character Hikari's Palace, and she suffers from near-crippling C-PTSD from almost everyone in her life trying to discipline the individuality out of her, which these movies functionally embody and depict.
The designated villain of the first movie is YOU, the Phantom Thieves of Hearts, with the Designated Hero being Kamoshidaman, the mighty superhero and "protector" of Kamocity. Since you were seen as an intruder, Kamoshidaman kidnapped Makoto and Haru. And seeing what kind of person Kamoshida is, things don't seem to go well with you, the villain....thankfully for you, he isn't Kamoshida and is just a bully terrorizing and occupying a city inside a movie, so he's just punishing criminals. Aside from that, you did nothing wrong other than entering his reality in the first place.
The designated villain of the second movie appears to be the carnivorous dinosaurs terrorizing the herbivore dinosaurs, which seems to be quite normal. In reality, the movie quickly displays that the carnivorous dinosaurs are just backdrops and the true designated villain is Yosukesaurus, a herbivore dinosaur with Yosuke's head. His crime? Not following with the Hive Mind and telling the other dinosaurs about a nonexistent "paradise" that he probably doesn't know in the first place. His punishment for this is to be ostracized from the pack, which drives him to the Despair Event Horizon and turns him into a carnivorous dinosaur resembling Shadow Yosuke.
The third movie has the most dubious choice for a villain in a movie. It's just a Cute Aigis Lookalike whose sole crime is to develop emotions and personality, in which the protagonist, an omnipotent AI has to remove so she can't start any wars. And for the crime of having a personality, her punishment is to undergo initialization and returning into an Empty Shell to be scrapped in the center disposal area. How fitting it is, then, that the central AI resembles Shuji Ikutsuki, whose mentality makes him the perfect fit for the AI Overlord.
The Frontier: While anyone who has played Fallout: New Vegas will agree that General Oliver isn't a nice person by any stretch of the imagination, the mod paints him as the villain for refusing to release the conscripts when a major war has just started and the NCR is barely holding onto Hoover Dam following the Legion's surprise attack. The fact that the Exiles defend Blackthorne by saying he led them to the Frontier to keep them safe and he had no idea the Legion would show up and attack them feels like a Double Standard, considering the fact that Oliver also had no idea the Legion would attack them.
Them's Fightin' Herds: The predators, from what we've heard of them, appear to be just trying to eat and survive. While it's understandable that the herbivores want to protect themselves, getting banished to another dimension is kind of an extreme punishment. In the October 10th livestream, Ms. Faust herself acknowledged this, saying that while it's true that the predators have to eat other creatures to survive, from a herbivore's perspective such actions are vile. She also explained the predators were originally planned to be straight villains until the fans began bringing up this trope, and that the final game "wouldn't be all black and white". It's also pointed out the Predators that were banished were ones who ate sapient prey, while those who don't were not.
Dance Dance Revolution Mario Mix: The Freezie in World 4. Toad tries to reason with it to get the Music Key back, but gets no response, since Freezies don't talk. He then says that the only way Mario can get the Music Key back is to kill the Freezie, which comes off as massive Disproportionate Retribution for being ignored, especially since the Freezie is the only boss in the game who doesn't actively antagonize Mario and Toad.
Fire Emblem Warriors: Three Hopes: Rhea can come off as one in Golden Wildfire. Compared to Crimson Flower of the original game, where she has undergone serious Sanity Slippage, takes an increasingly uncompromising and extreme approach to the war, and appears more explicitly responsible for the mismanagement of Fodlan, Golden Wildfire's conflict between Claude and Rhea is much less convincing in the eyes of many fans. This is because, despite Claude's assertions that Rhea keeps Fodlan shackled to the past and isolated from the outside world, the game does little to demonstrate this in practice: in fact, much of the detail on the setting and surrounding countries that was added in Three Hopes to flesh out the world shows ample evidence to the contrary. This is not helped by the fact that Rhea has essentially no presence within the route and thus has no opportunities to provide evidence to support Claude's arguments. Furthermore, in the endgame, rather than enacting punitive vengeance like in Crimson Flower, her last speech has her sorrowfully elaborate on her desire to protect humanity and beseech Seteth to flee with Flayn rather than expect them to fight to the death. Combined with Claude's morally dubious actions throughout the second half of the route, certain players can wind up sympathizing with Rhea more than Claude.
Dante's Inferno: The first three bosses. Death is... well, Death, Charon is just there to move souls, and King Minos only sorts the souls into the proper circles. Not terribly glaring, though; no one likes Death when he visits, the other two "work" for Hell regardless, and all three got in Dante's way.
Banjo-Kazooie: Conga. Whereas other foes in the series either try and kill the pair over a Jiggy, one of Kazooie's usual insults, or for not handing over a pizza they don't actually have, he just chucks oranges at 'em for trespassing in his home. And unlike most bosses, three Jiggies involve causing his misfortune instead of one: there's one for making him attack the orange tiles, another one for stealing an orange and giving it to Chimpy nearby, who helps them out by raising a stump, getting them to where they can attack him with eggs for the third Jiggy. Rare seems to have agreed as he's an ally in Banjo-Tooie.
and their only modern warship was built with Alpha Quadrant technology). Plus, their method of reproduction, basically necromancy, has drawn many rape comparisons, especially given that they're holding several thousand Vaadwaur cryo tubes and using the failed ones for more stock, along with making use of Vaadwaur battlefield casualties. Gaul jumps off the slippery slope in "All that Glitters", but the storyline reveals that the Vaadwaur high command are all infested with Puppeteer Parasites except for Gaul, suggesting they wouldn't have willingly gone along with his plans.