2027: Titan will reference this if you initate the Vladmir ending.
In Shin Megami Tensei: Strange Journey, most of the humans and demons are mostly cool with each other. Humans from your investigation team tend to go somewhere between Lawful Neutral and True Neutral, and the demons swing in a true diverse fashion, with virtually all alignments represented. Then again, demons like Mitra appear. Turns out, Captain Jack and his all-too human pals are way, way, way, too on par with Mitra for comfort, butchering demons (and by their willingness to torture and kill Jimenez, humans too) to create their own demon army. Especially when it turns out Jack and co. are Only in It for the Money.
ALL of the demons (or near all of them) are very quick to point out that while the Schwartzwelt is essentially a hell on earth, all of it is modeled on humanity's being a race of bastards with the innate instinct and talent for killing (Especially killing other humans). The more wild/bloodthirsty demons clearly state how awed they are by that aspect of humanity with a grudging respect/obvious distaste.
After a while, having every single demon you try to negotiate with asking "Why do humans suck so much?" gets tiresome... (Though they also like to ask, "Nice suit! Where'd you get it?", so...)
In Shin Megami Tensei IV, Lilith has the protagonists go visit a major Ashura-kai facility to witness what she, a Chaos-aligned demon leader who believes very much in Might Makes Right, considers "true evil". Said evil consists of Ashura-kai henchmen kidnapping fellow humans and making them into "seedbeds", extracting their brains in order to make the demon-quelling Red Pills, an act that disgusts the heroes more than almost anything the demons do in the game.
In the MOTHER series, the Big Bad alien conquerer (Giygas) is usurped by his own henchman Porky, a local bully who lives next-door to the game's hero. Giygas, however, has become a casualty of his immense power. Rather than risk destroying the universe he seeks to rule, his incorporeal form in placed in a Restraining Bolt device which is guarded by Porky..... who promptly releases the lock once you deplete his HP. He would rather destroy all existence than lose to the hero.
Though there is also Philemon, The Crawling Chaos' rival, who incarnates humans' positive aspects, and who may embody this trope even better than Nyarlathotep, in his own way - you kinda expect the personified essence of humanity's evil to be a total asshole, but you don't expect his opposite to be as colossal a dick as Phil.
The third and fourth games, however, focus on subverting this - the protagonists associate with those around them, discover the core of strength that lies at the heart of humanity, and use it to smash in the face of an unGodly monstrosity. Heck, this is made explicit in Persona 4, where the final boss reveals she was using three people to test humanity - one representing despair, one representing destruction, and one representing hope. You were hope, and as you finish her off, she declares, "Children of man... Well done!"
Given how prevalent this trope is, it's worth noting that Konami's Suikoden series averts it—the kobolds are largely portrayed as personable, but elves and dwarves tend to be very arrogant and xenophobic, and although most of the villains have been humans, it seems to be because they're more numerous rather than because there's fewer bastards in other races.
In Lunar: Eternal Blue, Zophar, the god of destruction, also believes in this. Lucia doesn't directly fall under this trope, but being an Emotionless Girl who is a servant (or something) to Althena that is required to sleep on the abandoned Blue Star for thousands of years gives her the impression that Althena alone is the only one capable of keeping Lunar at peace and in line. Character Development ensues as she adventures with Hiro and the others, and she, too, begins believing in the opposite trope.Even Ghaleon, the former Big Bad, returns realizing that the human strength that Alex had and that Hiro has are special.
Subverted in the Unreal series. Humans are bastards, sure, they run bloody sport competitions... but the Skaarj, a race of violent, xenophobic, savage reptiloid Bee People who believe all races besides Skaarj are inferior and exist solely to be reduced to slaves or wiped out for their amusement — or both at once — are bigger bastards by far.
While it doesn't have this theme per se, the racial backstory in Dungeon Siege II doesn't exactly put humans in a positive light. It says that the human race has a dual nature, but it only mentions the negative, not the positive; it says that humans are extremely violent.
To be fair, there's the Dryads. You'd think that a race of attractive plant girls who have an innate connection to nature would be some of the nicest people around, right? Guess again. Most Dryads are quite militaristic (more so in Broken World), and are unusually suspicious of other races, especially the Half-Giants (though the Elf Amren seems to be on good terms with them). Plus there's that Ring of Submission they have, which senses your intentions before you've even thought of them and then does painful or even fatal stuff to you accordingly. For a race that doesn't like government, that's a pretty fascistic way to treat your prisoners.
Thankfully, there is an exception: Taar. She actually is one of the nicest people around and isn't all that fond of the Rings of Submission (which explains why she's glad to remove the player character's). In addition, since as of Broken World, the Overmage is dead and peace is slowly but surely returning to Aranna, only time will tell if the other Dryads will also lay off the testosterone.
This happens a lot in StarCraft. For example, Arcturus Mengsk is a Magnificent Bastard at best and a Machiavellian despot at worst. Kerrigan is at first horrified when she's left behind, but when she gets turned into a Zerg, she actually enjoys it. Plus a lot of Terran missions revolve around Civil Warcraft. By the end of the StarCraft storyline, there's only one good Terran left among the notable ones: Jim Raynor. Thing is, there are only two other races and they are pretty much the same, give or take.
Or to be exact, the Zerg overmind desires to kill/infest the human colonists... and the Protoss attempt to stop this by burning the worlds... while the people are still on it. The Protoss burn them not because it's the only way or even the best way, but because they found humans distasteful but didn't have an excuse to remove them until the Zerg came along.
Starcraft II does a much better job of showing Terrans as a mostly good race, it highlights Acturus Mengsk's Villain with Good Publicity, while following the exploits of a force mostly made up of idealists. The General that follows Valerian Mengsk is also willing to work with Raynor with no real objections. This is because the game is about how even when things look darkest, there is always the light of hope.
Furthermore, both Brood War and Starcraft II shows that humans and protoss at the very least are Not So Different. The existence of a Dark Templar society and the Tal'Darim shows that the Protoss are just as prone to factionalism as the Terrans. Both races are slowly learning to distinguish friend from foe (The Khalai protoss respect Raynor's service to Aiur and skill as a commander, but still are hostile to the Dominion and the UED, while the Tal'Darim and the Dominion are hostile to all other factions, Terran and Protoss alike.)
The books that introduced Arcturus's son Valerian show him as a pretty decent guy with a passion for history, while his father only focuses on the practical. About the only thing the father and son can talk about is Valerian's collection of antique swords, which Valerian sees as art and Arcturus sees as weapons. This is likely because he was mostly raised by his mother, while Arcturus was busy defeating the Confederacy and setting up his empire.
Warcraft shows many humans who are pigheaded and prejudiced against races they view as "savage", and if a racist character shows up, it's more likely than not to be a human. But like other examples on this list, the other races in the world have their own prejudices and this was done to add some Gray as the early games were mostly Humans Are Special vs Always Chaotic Evil.
The fairies in the world of Drakengard subscribe to this viewpoint. The protagonist only ever meets two fairies, one of which is the king of fairies, and both of them, besides being annoying, feel this way towards humans to the point of being racist. Humans are big, dumb, ugly, smelly, stinky idiots to the fairies who can never get anything right and always destroy the forests to feed their infernal greed. When it comes to brass tacks, Leonard's Pact partner is an even dirtier coward, and has a Villainous Breakdown in Ending C when she realizes that Leonard is about to perform a Heroic Sacrifice, which due to their link will kill her as well.
Caim's dragon is also of this prejudice, but then again, dragons being arrogant and looking down on humans has pretty much been done to death.
NieR: Automata: This trope is mixed with Your Approval Fills Me with Shame when two Machine faction leaders list the various violent traits of humanity in a positive light - specifically, that all these horrible things are what make humanity such a fascinating and cultured species, compared to various alien civilizations which reached the singularity faster than humans invented the wheel, but had the cultural capacity of spoiled children and stayed that way. So the machines start emulating this human culture. Cue fourteen robot wars.
At least in this case the problem didn't seem to be blamed on humanity being evil, but that humans were heavily influenced and manipulated by Lavos, who uplifted mankind to the top of the ecosystem for its own purposes: to eat it.
They are also called out by the Dwarves who kill the faeries because humans accidentally poisoned their home. Clearly accidentally poisoning someone's living place is worse than actual genocide. Really the only people who has any right to call out humanity are the demihumans of Marbule as they never tried to kill anyone else.
This gets especially jarring when the human heroes are misblamed by the fairies they just saved from the genocidal dwarves. Dwarves blaming humanity for their need to wipe out the fairies to settle on a pretty large island is already Insane Troll Logic (especially if you consider that their Green Aesop is completely broken by the fact that they use smoking steampunk tanks). The fairies pulling the Humans Are The Real Monsters card in front of their saviors, completely blaming the dwarven invasion on them instead of, you know, the dwarves however is completely mind-boggling.
In Chrono Trigger every race got a chance to be a bastard, with the Reptites and Mystics waging wars in different time periods with the intent to wipe out humanity for ill-defined reasons. Even if humanity committed atrocities in the backstory that's a little extreme. The nature-based empire from Cross was the evolved form of the Reptites from Trigger which, to exist, likely killed off all the humans in their own timeline where Lavos never landed. Of course, it's humans that defeat Lavos and Save the World in the end (albeit with help from non-human allies.)
And that is not the only example to be found when it comes to the Tales Series. In fact, this is a major theme of Tales of Rebirth (along its Fantastic Racism), but the message is not "humans are bastards" as much as it's "all people, Humas and Gajumas, are bastards period". They hate each other because they do, and both do pretty nasty things to each other (some Humas refused to give medicine to a Gajuma woman while she was dying in front of her daughter, and some Gajumas chased an old couple out of town, forcing them to live in the middle of a desert filled with monsters). They get better... sort of. The end of the game implies that they keep on being douches, but at least the powers in command are doing something about it.
Duke did have this view in Tales of Vesperia, although the Krytians were just as guilty as humans were of summoning the Adephagos. And not all of the Entelexia were good, after all.
In Tales of the Abyss, humans were bastards but only to the replicas - which all had an Uncanny Valley effect on the populace. (Well think about it...if someone who looked and sounded exactly like your dead friend showed up at your friend's funeral, you probably would be a bit freaked out too!)
Tales of Legendia uses something like this as a plot twist. There are two types of people on that world, Ferines, the people of the sea, and Oerines, the people of the land. The game highly drops a lot of hints that one of them wasn't exactly native to the world. Naturally, you assume after seeing the technology in The Legacy that the Ferines weren't native. However, it's revealed in a surprise twist that it's actually the Oerines who are the aliens who came to the world in The Legacy, not the Ferines! They don't need land - they live in the water after all. Despite that in the past, one of the Human Groups Were Bastards, but so were the other to get revenge, and in that only some were bastards. (Quite a bit of the Ferines even want to start opening up peace talks again, once the Raging Nerifes was calmed down and replaced with the alter ego, the Quiet Nerifes, later called the Great Nerifes.)
Tales of Symphonia is also full of Fantastic Racism. It starts out showing half-elves, in the form of Desians (who are running human ranches all across Sylvarant) are the bastards, and the humans are the victims. But because of their treatment by the Desians, humans are bastards to half-elves. It slowly starts showing how much humans can be bastards as the party reaches the parallel world of Tethe'alla. Skip to deeper in the game, and it turns out that the reason half elves are bastards is because the angels, who command the half-elves, are also bastards. And the reason the angels are bastards is because the big bad: Mithos Yggdrasil. Mithos' older sister Martel is killed by humans four thousand years before the story takes place, which in turn makes him obsessed with reviving his sister. And pure-blooded elves were also plenty racist to half-elves, casting them out of their Hidden Elf Village (Genis and Raine aren't even allowed in when you first visit.)
In the same note, Tales of Phantasia has the elves once again hating half-elves and humans. They distanced themselves from humans when they began to work on the Mana Cannon, a powerful weapon that uses up the world's mana and will cause the world tree to wither and die, and have since been living in their village, refusing contact with humans unless they have royal permission. Their exact reasons for their hatred towards half-elves is never really explained (it could be because half-elves who do not grow up among several elves do not have the same values, perhaps) but it is much more intense than their hatred towards humans. Half-elves are not permitted in the elven village, any half-elf that does enter the village will be killed, etc. Though when you return in the future time, 50 years from the present, the leader of the elves Brambard does reveal that they are improving themselves, allowing humans to enter the village without royal decree, but half-elves are still forbidden. Then you recall that Phantasia is supposed to be a very distant sequel to Symphonia...
Humans in the PC game series Age of Wonders almost always have leaders whose favorite pastimes include leveling elven forests, siding with demons and orcs for more power, and enslaving lesser races. This is despite the fact that they technically have a "Neutral" alignment.
In the sequel, however, they're mostly being manipulated by a vindictive Water Wizard.
The Therions (anthropomorphic animals, ranging from lion-men to gazelles to rhinos to panthers) of Jeanne d'Arc deeply resent mankind, a hatred stemming from how the very humans they assisted in the Demon War turned on them and corralled them all up in a tiny warren just outside Paris (where, previous to the war, the Therion kingdom extended all over Europe.) In fact, the few Therions that assist Jeanne and her cause are a minuscule exception to the rule.
The LucasArts adventure game The Dighung a lampshade on this issue. When one of the characters tentatively points out to a friendly alien that not all humans are as nice as they are, the alien cheerily replies that that's okay, since all relatively young species are like that, and anyone who wants to pick a fight will just be squashed like bugs.
Dracula from Castlevania likes to toss out this accusation to whatever Belmont he's fighting, usually starting by mentioning that the only reason he's up and about is that some human woke him again. But the Belmonts are generally full of righteous fury and in no mood for discussing the idea, so not much comes of it.
What is a man? A miserable little pile of secrets!
In some games it's explicitly stated that Dracula's continuous resurrections are not just because of individual Dracula-cultists resurrecting him, but that human malice and greed in itself allows him to continuously come back even when it isn't his will to do so. This may be more As Long as There is Evil rather than an endemic thing, however.
Dracula does have a Freudian Excuse relating to this trope, having lost at least two beloved wives to human cruelty. The death of the first to illness while he was fighting in the crusades led him to renounce his humanity and declare war on God, and the death of the second one to a witch-hunt caused him to extend that war to humanity. His reincarnation follows the same path if the player lets his girlfriend die.
Final Fantasy VI. The Espers lived in a lush and fertile world in peace and harmony with themselves and their surroundings despite the fact they can use their magic powers for destruction, while the humans drain the power of the Espers into delicious whiffs of magic purely for warfare and personal gain, going as far as to modify their own bodies with a sickening blend of their own technology and their magic extracts of the Espers. The two largest human cities in the game, Zozo and Vector, are also completely terrible places and both have little to no redeeming qualities within them whatsoever.
In Final Fantasy XII, you can't swing a dead cat without hitting some non-human eager to remark on how power hungry we are, with a distinctly condescending and pitying tone. What nobody seems to mention is that while humans love to start their wars, they're also the only ones able to stop them, precisely because they're willing to wield power against power.
Also used with a Viera after Judge Bergan's attack on Mt Bur-Omisace. Many people are injured or dead and some of the humans are begging a Viera to help them, but she refuses because she sees the humans as nothing but power hungry maniacs who kill everyone, including their own. But after you kill the optional boss Fafnir, you learn that Ieeha, a human, had sacrificed himself in an attempt to defeat the monster. Upon learning this, the Viera realizes that humans can be good as well, and begins helping the injured with her knowledge of medicine.
The game either tries to mitigate this or is hopelessly hypocritical in that at least half of the other races (besides Viera) are not just criminals, but scum sort of criminals like slavers. And the Viera themselves are basically just a reskin of Enterprise era Vulcans in their manner.
Shows up again in Final Fantasy XIII. Your party spends a good chunk of the game on the run from the Evil Army while everyone else on Cocoon hates and fears you, even little kids. The populace of Cocoon even support complete Purges of residential areas where L'Cie have been spotted due to their extreme paranoia concerning anything Pulse related. To be fair, most of them only act this way because they believe Pulse L'Cie are horrible monsters that want to destroy everything they know and love. Furthermore, the Fal'Cie are the ones actively nurturing the populace's worse traits to lead them to destroy themselves. The only human portrayed to be a total bastard is Jil Nahbaat. Dysley's a bastard too, but he's disqualified since he isn't human.
Lineage II also has this to an extent. While the other races are pure and beautiful children of the elements, humans were made from the corrupted remains of each, and upon their creation, were immediately recognised as scum by everyone save their twisted creator.
This is quickly subverted in that the humans were enslaved by the other species and treated like trash for being second best at everything. Which won them the war in the end. ""So. Is it not ironic that the lowest creatures of all, the humans, ultimately attained ownership of the land? But that is the result of human will. Even the gods did not imagine that humans would ever become rulers of the earth."
B.B Hood of Darkstalkers fame, the only perfectly ordinary human in the entire cast of monster-people, is arguably the biggest monster of them all. The point of her character is to exemplify human evil.
In the Star Control universe humans are hardly one of the evil races, but they have had their... poor moments. They designed a race of super-intelligent clones, the Androsynth, then declared them inferior and put them into manual labor. This backfired rather spectacularly when the Androsynth, being more intelligent than your average Joe, still invented hyperspace travel before the humans, escaped, and eventually joined the Ur-Quan Hierarchy, hoping for some sweet revenge.
Oh, and humanity also managed to collectively alienate the VUX by insulting their appearance in the first contact - ironically, humans look just as attractive to the VUX as the other way around (VUX is sometimes treated as an acronym for "Very Ugly Xenoform"). This would lead to a massive political crisis and, indirectly, to the VUX joining the Ur-Quan as well as, isolated, they could not match the Hierarchy. So out of 7 races in the original Hierarchy, humankind is responsible for two. Unsurprisingly, the Alliance (which humans were members of) eventually lost the first war.
...And the VUX example is subverted when we learn that the "won't forgive you because of The Insult" is an excuse, but the real reason is they find us so repellant that they never even considered not going to war with us. So really, humans may be foul-mouthed bastards, but the VUX are just jerkasses.
Subverted in Soul Nomad & the World Eaters with Nereids (Juno in particular). Their view on humans is more like Humans Are Untrustworthy rather than full on Humans Are The Real Monsters. An extra level of subversion kicks in as unlike many examples of this trope, they're more willing to judge on an individual basis. The ones that pass are seen as potential mates. Despite being on opposite sides, Throndyke is still respected as a good man anyway.
Played straight since according to the official site humans are largely responsible for the tradition of war and conflict on Prodesto.
Subverted and parodied (in a straight manner) in Elven Legacy. The main characters, who are elves, will often (oh so often...) go on a rant about human bastardness, while at the same time acting either in equally bastardly manner or topping humans by quite a bit. Most blatant when the protagonist accuse humans of arrogance for daring to think elves would be humble enough to surrender their weapons and meet with their lord.
Humans' potential for Bastardry is the reason the Aerogaters and Inspectors attack Earth in the Super Robot Wars games in which they appear: The Aerogaters wish to turn us into brainwashed soldiers, while the Inspectors fear us becoming a threat, and try to keep us under control.
In the Toe Jam And Earl series, where humans and other earthly life aren't wantonly malicious and "unfunky", they're still weird. Friendly ones in the series include the Wiseman in a Carrot Suit and the Soul Sisters — a trio of black women who speak only in gospel song. In Toe Jam & Earl 3, you can convert most initially hostile Earthlings... such as chickens with army helmets and egg-firing mortars, and Creepy Child little girls with seemingly demon-possessed teddy bears. See? Weird.
A major plot point in Arcanum: Of Steamworks & Magick Obscura, where humans have triggered an industrial revolution with dwarven technology acquired by Arcanum's richest businessman Gilbert Bates. As a result, the Forest of Morbihan has been transformed into the Morbihan Plain over a few short years, and the most industrialized city, Tarant, is also one of the most polluted. Members of other races such as dwarves and elves theorize that because humans have relatively short livespans, every action they take is motivated by the fear of their impending deaths, and they do not live long enough to see the consequences of their actions.
Revealed in one dialogue during Mega Man Zero 3, stating that humans of the dystopian Neo Arcadia only indulge themselves in food and comfort, letting the authorities do the thinking for them while regarding the conflicts Zero and Ciel have been fighting as mere daily news on the televisions. In Z4, Zero also further condemns humans fleeing from Weil's iron fist as cowardly beings who would do nothing about their refugee leader getting kidnapped just to avoid another war. It is not until Craft blows up the city do humans finally wake up with terrible pain in their minds.
Dr. Weil also implies in Zero 3 that Humans innately feel that ruling all the eye can see and making others work for them is the ultimate joy for them, and believes that no Reploid could ever understand this joy, although Zero counters this by stating that he doubts any decent human would understand Weil's viewpoint, either.
There's also the fact that Weil, the single most vile villain in Mega Man canon, is a human.
The plot of [PROTOTYPE] is about a viral infestation that threatens Manhatten and potentially the world. The citizens' only "hope" is Blackwatch, an army of bastards who kill both infected and healthy people. You later learn that your character is not really Alex Mercer. The real Alex unleashed the Blacklight Virus out of pure spite and died before the game began. The Alex we know is actually a personification of the Virus itself that copied Alex's genetic makeup. The Virus is absolutely disgusted that it's own creator let it loose on the world and spends the entire game essentially trying to save the world from it's own infestation and is even willing to sacrifice itself for the planet. When the Humanoid Abomination who was created specifically to destroy the world ends up being the most sympathetic and heroic character in the game, you know Humans Are The Real Monsters.
In the [PROTOTYPE 2], Mercer's growing disgust with humanity's flaws drives him to become a Dark Messiah bent on uniting the entire world into a Hive Mind so he can end all conflict.
Casually tossed here and there in Kid Icarus: Uprising. Palutena notes, when talking about Magnus, that humans are fundamentally driven by desire, using the mercenary as an example. Hades gets humans to go to war with themselves to an insane degree by spreading the rumor of the Wish Seed. This draws the ire of the nature goddess Viridi, who begins attempting to annihilate humankind for their greed, violence, and wastefulness. It's ultimately subverted in that the other sentient race, the gods, are shown to be just as bad, if not worse.
How humans in the Mass Effect universe may be seen by the other races. Within 30 years, humanity has rapidly expanded and forced our way to the top of the galactic government which has existed since we were in our bronze age.
Some of the human factions and characters easily qualify as this, especially Cerberus.
Inverted in the sequels. In Mass Effect 2, it's revealed that despite the fact that a Reaper attacked the in-universe equivalent of the U.N. headquarters, the Council refuses to take any steps towards preparing for the imminent Reaper invasion. Cue Shepard going 'rogue' and working with Cerberus. In Mass Effect 3 this is taken even further. It's revealed that the Salarians DID take Shepard's warnings seriously but not seriously enough to push the Council into action. The Turians only took Shepard's warning seriously after the invasion began and, assuming he survived the events of Mass Effect 2, recruit Garrus as a 'Reaper expert'. The Asari not only ignored Shepard's warnings, its revealed that they were concealing a fully operational Prothean data beacon not only capable of warning about the Reaper threat but containing vital information to building a weapon that could defeat the Reapers. AND this is on top of the fact that the Asari have effectively ruled the galaxy for centuries, which one of your teammates will point out. To add insult to injury, this is the same galaxy ruling species that passed laws forbidding withholding Prothean technology.
It should be pointed out that both Humans Are the Real Monsters and Humans Are Bastards in addition applies nonetheless if you choose the Renegade path at the end of Mass Effect, what with ordering the human fleets to stand back at first, and thereby sacrificing the Destiny Ascension, which was evacuating the Citadel Council, and thus, the entire Council in cold blood. The intra-human "bastard" part comes in the form of the new Council, now headed by a human, still not giving a damn about Shepard's warnings (that the human Councilor is the Jerk Ass and, later, Cerberus sympathizer Udina probably is a factor). But basically, it depends on play style - a full Renegade playthrough will hammer home just what kind of monsters and bastards humans are, while in a Paragon playthrough, things are looking much nicer.
The villains of the Orochi Saga in The King of Fighters, namely the aforementioned Orochi and his followers, strongly believe this. To them, humans have ruined their world&the environment, though aside from that, they don't consider them all that great in general, to the point where they believe humankind should be annihilated. (Though part of this may also be that they serve a higher power, 'Gaia', but regardless of whether or not they're being influenced, this is still what they believe.) The Edit-Team ending even outright states that while Orochi still needed to be stopped, humanity still wasn't that great either, and that we were partially to blame for Orochi's purpose being twisted into what it became. Still, some of our heroes (as in, the various teams,) acknowledge this to an extent, though they don't think that humanity is completely un-redeemable.
Another work of SNK's, The Last Blade (technically set in the same universe, but in the 1860's in Japan), has a similar villain. Kagami is one of four individuals that were gifted with powers by the four Japanese Gods, with Kagami representing the phoenix, but with time, Kagami grew disgusted with humanity, and with that belief in mind, got to work opening the Hell Gate, with the intention to suck Earth into Hell. In the sequel however, he's reborn, (after being sucked into Hell's Gate in the first game,) and by the end, after being forced by the God's into service once more, decides to personally give humanity a second chance.
Being in a Crapsack World, everyone everywhere in The Witcher could be called a monster, whether its humans for oppressing nonhumans, elves for creating their own terrorist army that kills civilians and steals from hospitals to fight this oppression, or witchers themselves for taking just about any job if it pays since the decline of the monster population they were originally built to fight. However, the end of the game sums it up pretty well when Geralt is about to kill the Big Bad Jacques De Aldersberg with his silver witcher's sword after Jacques knocks away his steel one with magic. Jacques protests saying, "But... that sword... it's for monsters." Geralt's response is to silently stab him in the throat with it. While the witchers' silver swords are more suited for killing supernatural creatures and their steel swords more suited for killing humans, Geralt believes that "both are for monsters."
The first quest of the game shows that regular, unassuming people can be just as bad as the murderers and zealots. The town guard who is mourning the beautiful young woman who passed away? It's implied that she took her own life because he raped her. The fat merchant living on the outskirts of the village? It's implied he murdered his own brother to get his coin. The kindly young witch who helps you through the quest? She's actually a devotee of a psychotic death cult. Depending on who you ask, either one could be directly responsible for The Beast haunting the village.
The trailer for the third game has Geralt collect his pay from a witch hunter whose cohorts are in the middle of hanging a girl from a tree. Just as it seems Geralt is going to just ride away and leave the girl to her fate, he dismounts his horse, kills all of the witch hunter goons in less than a minute, and cuts the girl down. He then walks over to the cowering man on the floor and grabs him:
The backstory for Paladog has humans filling the world with so much evil that the gods are forced to destroy the world and create a new one with critters as the dominant species. Under the rule of the critters, the world becomes a utopia almost entirely devoid of violence... until The Legions of Hell invade it because they couldn't manipulate the crittier's minds like they could humans.
In Dragon Age: Origins, humans have done some terrible things. Currently, many elves are former slaves who still have second-class citizen status and lives in city slums. Their Dalish cousins are forced to constantly live a gypsy-like lifestyle and move their camps every few months or so. They still remember their old civilization, which was wiped out by Knight Templar humans because the elves refused to worship Andraste. Subverted in that the elves also had their bastard moments, such as their first civilization trying to conquer humans. Then there's the Tevinter Imperium, where the ruling magisters can do whatever they please.
In Dragon Age II, due to continuing mistreatment by overzealous Templars, many Mages are forced to resort to Blood Magic to either try to escape or simply protect themselves. However, this only creates a vicious circle as the Templars use this as proof that they need to tighten their choke-hold over the Mages. Eventually, the events at the endgame push the Mages too far, causing every Circle in Thedas to rise up and declare all-out War!
Sebastian: What do the Dalish teach about the creation of the darkspawn? I mean the Chant of Light says it was the hubris of magisters trying to compete with the Maker. But you don't believe in the Chant of Light... or the Maker. What do you believe? Merrill: Well, we don't get into many details, but we're pretty sure it's the humans' fault.
Dragon Age: Inquisition reveals in its latter half that humans had little if anything to do with the destruction of the Elven empire. The Elven empire was brought down by Civil War- the human slavers came in to loot and pillage years after the dust had settled and Elvish society was in ruins, "picking over a corpse".
Shows up as graffiti in the "Dead Air" campaign of Left 4 Dead ("WE ARE THE REAL MONSTERS!"). Also mocked right after ("Have you been outside JACKASS!!"). They really miss the internet.
Shows up again in "The Passing", as a piece of commentary on bathroom graffiti. "I flushed it 50 times and now it DOESN'T WORK!","You IDIOT! YOU ARE THE REAL MONSTER"
Gentleman Adventurer Sir Hammerlock asks you to investigate why the giant Crystalisks (giant tripedal rock-like creatures with crystalline formations on their legs) have become so violent, when they were previously quite docile. It turns out that the Crystalisks did not particularly appreciate having their crystals "mined" off of them by workers from the Dahl Corporation, since without those crystals, the Crystalisk dies. In a prolonged and explosive manner. As the Crystalisks are highly resilient to small arms fire, things get very messy for Dahl, and the Crystalisks now regard just about anything as a potential threat to be exterminated with extreme prejudice.
To twist the knife, you hear one sympathetic Dahl employee's ECHO where she plays with Blue (A rather large Crystalisk) with her hat telling Blue to wait a moment. She ends up getting killed by her boss when she tries to defend them.
Chief:[growls heard in background] BLUE! Not now. Here, go play with my hat. [laughs] There you go, Blue! Oh yeah we met a large one down here. She's very friendly. We call her Blue because... [clears throat] ...yeah.
Oh, not feeling the knife yet? How about the fact that the very same Blue is the mandatory boss-fight for Marcus's "Safe and Sound" quest? Meaning you have to kill Blue to get back Marcus's precious safe full of lewd photos of Moxxi.
While the TRON movies centered on A.I. Is a Crapshoot, Tron 2.0 went this route instead. The Programs were just trying to carry out their functions and mind their business when a small group of insanely greedy humans decided they liked the idea of virtual godhood a bit too much, and planned to conquer the digital world with an army of mercenaries, enslave the Programs, and rule the world from the shadows by blackmailing world leaders and manipulating global finance and media.
Mercury: This is no place for a User. We're too crude and rudimentary. Jet: If anyone's crude, it's us, we're not ready to exist here. Not yet, anyway.
In FTL: Faster Than Light, you'll encounter any number of aliens with unique abilties trying to kill you—the Mantises, the Slugs, and the Rockmen are three especially vicious species. Even the Zoltans will get pretty uppity over laws in their territories, and the generally-peaceful Engi can and will engage you in combat if they believe you to be trouble to them and their creations. But the Rebel faction that's out to destroy The Federation? It's comprised of humans. Yes, the same species described as being boringandaverage have amassed to big enough numbers and developed a strong enough fleet to pose a fatal threat to the Federation, and possess the single strongest ship in the entire game, the Rebel Flagship.
Played with in Ecco the Dolphin: Defender of the Future. When dolphins are made into non-sapient creatures by aliens stealing their ancestors' noble traits, humans take over the world, uplift dolphins, and immediately enslave and abuse them. However, when time travel causes the dolphins' ancestors to reattain sapience without the traits that make them kind, they take over the world and drive humans from the seas and probably to extinction, after which they abuse and enslave each other and whales. The takeaway message seems to be less Humans Are the Real Monsters and more Unchecked Dominant Species Are the Real Monsters - things only go well when humans and dolphins start a joint society as humble equals.
Discussed frequently in The Last of Us, where Joel has to face both infected humans and factions of barbaric humans. Especially so during the prologue; set during the outbreak of the infection, it ends when Joel's daughter is surprisingly killed by a soldier with shoot-to-kill orders.
Bill: Ya know, as bad as [the infected] are, at least they're predictable.
Beyond: Two Souls. Meet Jodie, a girl who can talk to spirits, and has a spirit attached to her. She is also suicidally depressed. Why? Because for most of her life starting from birth, the 99% of the humans she met either treated her like shit (her own father called her a monster in front of her, and that's ignoring the teens who threw her into a closet and called her a witch) or wanted to use her powers for their own selfish desires ("You will use your powers for our organization, Jodie!" or "Use your powers so I can talk to my dead relatives, Jodie!") There are, shockingly, very few people in the game that actually treated her just like anyone else, without being cruel to her, or planning to exploit her for her powers.
Played horrifyingly straight with Skull Face who takes a primordial species that facilitated the birth of human civilization and mutates them into an "ethnic cleanser", capable of killing anyone who thinks and acts in a certain way. He also uses research on fallout-eating bacteria, reverses the polarity (they now restore the uranium's radioactivity), and applies them to a Metal Gear made of depleted uranium. The end result is a Metal Gear that can be transformed into a nuclear bomb big enough to take out an entire country. So yeah, who's the real disease here?
In Dishonored, The Outsider makes more than one comment that strongly implies that he believes the "nature of man" to be cruel and corrupt. A nonlethal Corvo seems to incite his curiosity precisely because of this: Corvo is choosing, of his own free will, to act in complete opposition to everything the Outsider believes humans to be. The only time the Outsider is ever shown to be genuinely taken aback is if Corvo chooses to spare Daud. Regardless, it doesn't seem to change his opinion or even make him reconsider; rather, he indicates that he sees Corvo as the exception that proves the rule.
In the Dark SoulsDownloadable Content "Artorias of the Abyss", Hawkeye Gough and Lord's Blade Ciaran aren't terribly impressed with humanity. If the player chooses to attack them, they aren't surprised since they expected no better from humans. Even more telling, the most evil and vicious thing in the game is a human who has let his fraction of the Dark Soul, aka humanity itself, go out of control, turning him and the entire population of Oolacile into monsters. It's stated that if the Age of Fire ends, the Age of Dark will come, but apparently given that humans are Darkness, the Age of Dark would be a golden age for humanity... and this is not presented as a good thing.
The Dead Rising franchise has this a lot, as the bosses are all human and most are either insane or exhibit the worst qualities of humanity. In Dead Rising 2: Off the Record, Chuck Greene points out that zombies are so mindless, weak, and slow that defeating them should be child's play, but whenever an outbreak or other disaster happens, people give in to their greed, fear, etc and turn on each other.
Humanity is so twisted that by Dead Rising 4, the first-ever sentient zombie (made of a Hive Mind of insects living in the brain) declares war on the human 'Cycle' of insanity - complacent to revenge-driven to power-hungry back to complacence again.
Said word-for-word by Double in Skullgirls, as she is a herald to the Trinity, who created the Skullheart solely to prove this trope. Also played with on the fact that her base form is a nun.
In Mini Robot Wars, it's revealed that Star Travel Inc., the ones behind the evil Machines' invasion of the Minirobots' Green Planet, are humans who lost the "Blue Planet" due to their neglect.
Seems to be a major theme of the entire Five Nights at Freddy's franchise. Yes, the animatronics are trying to kill you, but throughout the backstory everything that led to this state of affairs: murders, pointlessly destroying animatronics, the Bite of '87, all were caused by humans out of pure cruelty.
Undertale purposely dances around this trope. For a while, it seems to be played straight. The monsters who initially try to fight you are easily won over by kindness, and even the ones determined to kill you and use your soul to free themselves from their imprisonment underground can't bring themselves to harm you if you refuse to fight back. Plaques fleshing out the details of the ancient war between humans and monsters give the impression that the war was a lot more one-sided than initially let on. Then there's this zinger from one of the books in the Snowdin Library, which could practically be the page quote for this trope:
Love, hope, compassion... This is what people say monster SOULs are made of. But the absolute nature of "SOUL" is unknown. After all, humans have proven their SOULs don't need these things to exist.
But on subsequent playthroughs, you learn that the Fallen Human you named at the beginning of the game, who is not the character you play as, felt this way for unstated reasons and sought to wipe out humanity — and their failed attempt at doing so led to the creation of the game's only true villain. On the other hand, that doesn't really change the human/monster dynamic, since the only villainous character who doesn't straight-up lack a soul is still human. Either way, the message seems to be that cynicism, and turning one's back on an entire species, will only make things worse for everyone.
Nihilumbra: Subverted in the City. The narration notes that whoever created the City destroyed whatever environment was there to build it...but then turns around and points out that even so, at least they created something; all Born has done, meanwhile, is allow the Void to consume the world.
The Turing Test: The ending where you don't kill Ava and Sara gives this impression. It's hard to not see TOM as the Doomed Moral Victor while watching Ava and Sara mercilessly shutting down his system piece by piece, ignoring his pleas for them to stop, all while he's got a gun aimed at them... but can't bring himself to fire.
Path of Exile: Every god you encounter is a Deity of Human Origin, and all of them but one are Jerkass Gods. Sin, the one god who valued humanity for more than being worshipers or food, created the Beast to drain the powers of the gods and keep them in an eternal dream state. Unfortunately, since the Beast fulfilled its purpose just by existing Sin did not give the Beast any ambitions or desires, leaving it vulnerable to human thaumaturges who tried to use its power for their own ambitions. Attempts to tap the Beast's power destroyed civilization across Wraeclast twice and left the continent steeped in corruption.
The twist regarding the Big Bad of the original Digimon World is that it's not Analogmon, it's Analogman, which is the screename of an adult human hacker who has discovered and invaded the Digital World, which he intends to enslave, convinced that Digimon exist only to serve humanity.