It is possible for the player to be this in any game that includes a morality system, if the player makes choices based on a line of reasoning besides good or evil. Of course, many games punish you for not being either all the way good or evil (for example, Infamous), or puts you in in the middle path.
The Caldari in EVE Online come off as this to pretty much everyone else. The Caldari's society revolves around their somewhat odd form of Capitalism, where every citizen and corporation is trying to increase their market share above all else. The Caldari state essentially lacks a government, and is a series of kingdoms ruled by megacorps. They are Cyberpunk taken to an extreme. Yet they are one of the most content groups of people in all of New Eden, because the success of their economy makes them happy, and everything that hurts the economy is immoral to them. None of the other Empire's understand this, and the Gallante have been at war with them since the Caldari succession because they simply don't believe the Caldari people could actually be happy under their oppressive non-government.
God of War: Ascension: The Furies are described by a note from the Scribe of Hecatonchieres as following "their own view of right and wrong;" their purpose is to track down those who have broken blood oaths with the gods, and punish them for it no matter what. Ultimately subverted, as by the time of the game, they're conspiring with Ares in his Evil Plan to overthrow Olympus using Kratos.
The Reapers of Mass Effect claim to have good reasons for annihilating all advanced species in the galaxy on a regular basis. In Mass Effect 3, they claim their cyclical process of destruction is a form of salvation and protection. Their primary directive is to prevent a technological singularity that will, they believe, cause synthetically created life to completely destroy organic life forever. To prevent this, they direct technological development at a pace they deem acceptable and then "reap" major civilizations at a specific point of development, around the invention of intergalactic travel and true artificial intelligence. Those civilisations who haven't reached this point by the time the Reapers arrive are left alone. The ones that have become new Reapers themselves, their knowledge and genetic material preserved. Any other sentient life, organic or synthetic, is obliterated. The Reapers retreat, and the Cycle begins again. The Cycles finally cease when a new way to "preserve" organic life is found, the form of which depends upon Shepard.
The Asari Justicars have their own extremely strict moral code that determines their every action. Though they fight what they perceive as crime and injustice, their code has no affiliation with and often contradicts Citadel law. Samara's recruitment mission in Mass Effect 2 and her appearance in Mass Effect 3(in which she is obligated by a Justicar Code technicality to kill her daughter, but instead chooses suicide, further complicating her morality) make these disparities clear.
Drell believe that you only bear moral responsibility for actions you personally choose to undertake - if you're following the orders of a superior, the weight falls upon them, and if you do something out of instinct, it's your body rather than your soul that is responsible. The main drell teammate you have is an assassin, who feels no guilt for any of his kills except inflicting a lingering death on his wife's murderers, because those were the only people he hunted down of his own free will.
Thane: An assassin is a weapon. A weapon doesn't decide who it kills. The one who wields it does.
He just flat-out kills M. Bison (or Vega, if you insist on the Japanese names) without a fight, because according to Akuma/Gouki's moral standards, he is as pure an evil as you can get. Trying to claim false power without actually working for it, falsely claiming to possess power you don't have, murdering people in cold blood without giving them the opportunity for a fair fight — all "sins" in Akuma's eyes, and the fact that Bison possessed all of them meant that he simply had to die, rules of fair combat be damned. The fact that Bison was also pure evil and deserving of death by the standards of normal people was just a happy coincidence. There's also the alternate theory that it was actually a big fight, but it was skipped over for the sake of the game.
He also refuses to kill Gen after defeating him in a battle, because he has a terminal illness and wants to die in a battle. Apparently in Akuma's view, that made it an "impure" fight and thus Gen does not deserve to be killed. Even more interestingly, the exact opposite happens in the comic, where he purposely kills Gen, precisely for the above reasons, as a Mercy Kill.
In Knights of the Old Republic, Mira has a very strange moral code. Apparently it is wrong to kill without good reason, but the best way of dealing with men is to knock them out, slap some stun cuffs on them, starve them for a few days so they're more open to suggestion, and double check to see if they have any bounty on them. This line of thought is hinted at earlier when she drugs you and locks you up but only after she tells you that you have a bounty on your head. (However, this is done regardless of your gender.) And she have actually been kidding.
In the MMO the light side/ dark side morality system can be this to the non-Jedi classes. If you play your character as motivated by anything but good for good's sake or evil for evil's sake (a soldier zealously dedicated to her duty or a Proud Warrior Race Guy bounty hunter for example) the alignment changes appear completely random.
Kreia's behavior in the sequel has shades of this. While she seems to be advocating a Grey and Grey Morality overall, she's so extreme in her opposition to extremes that it's difficult to really sense what she'd even consider a Moral Event Horizon.
Morgfyre of Lusternia was a Warrior God before he began devouring other Gods and numerous Eldritch Abominations. Unable to subsume their personalities beneath his own, he instead adopted them - becoming a gestalt entity, able to think with many different minds and speak with many different voices. Consequently his train of thought can be difficult for other Gods to follow, let alone mortals.
Depending on the writers, the Daedra can be beyond human comprehension, ambivalently moral, or just plain evil. Some individual Daedra have both good and bad aspects, such as Sheogorath, the Daedric God of Madness, Creativity and Artistry. Others are like Molag Bal, who is called the King of Rape for a reason. In fact, most of the Daedric Princes have good and bad aspects, or at least aspects that are not inherently evil from a mortal perspective. It's just that some (Mehrunes Dagon) tend to favour their bad aspects when they show up, while others (Azura) more commonly show a good side.
Actually Azura is much more like an incomprehensible cosmic terror than most other Daedra. The evil Daedra are at least predictable (CRUSH KILL BURN) while Azura is highly unpredictable yet very dangerous even as far as Daedra go, turning an entire race black as punishment for their lack of faith (and they still fanatically worship her). Her holy relic is the most powerful soul trap in the world even though her dogma has nothing to do with soul trapping or enslavement. Her domain is the hard to define "magic of twilight". And she has a mountain-sized statue in Skyrim.
The Magna-Ge, the children of Magnus. Very little lore exists about them and it reads like a shroom trip.
Alduin's role as the Big Bad could fall under this. His goal is to end the world, which most mortals see as a bad thing. The Greybeards just see it as fulfilling his duty as the World-Eater.
Similar to the Elves of Dwarf Fortress, the Bosmer, or "Wood Elves" find it unacceptable to harm any plant, to the point where they make alcohol out of meat and weapons from bone, but at the same time are perfectly okay with eating their own dead as a funerary rite or fasting before going into battle, expecting to devour their opponents.
Every character in Zeno Clash exhibits this to some degree. The Corwids more so than most.
None of the various factions in Thief are aiming for "good" or "evil" in the traditional sense. Every one of them has a different idea of what those words mean. The Pagans believe in pleasing their chaotic god, the Trickster; they plant growing things and encourage wildness and semi-feral, uncontrolled nature at its most unspoiled. Their magic uses weird sing-song chanting, blood, bone and herbs. The Hammerites work to please their creator god, the Builder; they enforce order and venerate works of the hands and the forge, bending wood and breaking stone for tools to build over and bind natural chaos to human dominion. Their magic is very Catholic-flavored, using holy water, prayer, symbols and ritualised masses. The Mechanists are an extremist offshoot of the Hammerites who won't even use wood in their construction, seeing it as heretical. Wood must be burnt to fuel works of stone and metal; all organic things are flawed and must be broken down. Finally, there are the Keepers, who have taken upon themselves to ensure that neither the Pagans nor the Hammers gain the upper hand, because (of course) the Pagans and the Hammers are in constant warfare. But even the Keepers aren't quite traditional - they have such a strict policy of non-interference, secrecy and heavily controlled knowledge that very few non-Keepers are aware they actually exist.
Wilhelm from Xenosaga exists solely to prevent the destruction of the Lower Domain. He does not care for how many lives he must manipulate, ruin and destroy to achieve this goal.
Touhou gives us Yukari Yakumo who, in addition to being super intelligent, has her own brand of logic that nobody really understands. Most of her conversations in Scarlet Weather Rhapsody are excellent examples of this.
Gensoukyou as a whole is an example of this trope, with things such as vastly extended lifespans and entirely non-lethal combat creating different standards of morality. It is completely insane to us to go out and beat people senseless because they aren't human or mess with everyone's lives because you were bored, but not to them.
Also worth noting is that youkai of various species and ethnicity are the majority population in Gensokyo, so things like eating humans (or other youkai) are not at all unheard of, and there have apparently been agreements on which humans are permissible to attack and eat (mainly humans who aren't in an established safe place at night).
Utsuho Reiuji. She's a hell raven, which means that her natural habitat is something that is hotter and more radioactive than if not close to the sun. When she's given the power of a dead sun-god, she decides that the whole world should be an ever-burning nuclear wasteland. Why not? It's what passes as ideal for her, and she cannot fathom why anyone would ever want to live in a world of clear water, greenery and cool breezes. Of course, however, this cannot really be helped as she isn't very bright and developed more of this morality when she was given the power of the dead sun god in the first place. Too bad most people (In-Universe and out of it) only see her as a genocidal crow.
Kazami Yuuka. Generally, she is peaceful and polite. If she is disturbed in any way, she is consistently recognized as one of the most dangerous beings in Gensokyo. The problem is figuring out what disturbs her. Abusing flowers: death. Running a flower shop, where they are cut up, arranged with other cut flowers and left to die: perfectly okay. If you are weak and don't disturb her, she'll ignore you as not worth her time; antagonize her, and she kills you. If you are strong and disturb her, she happily challenges you to a formal but non-lethal duel. When accused of being behind an incident, she makes no claims to be innocent, even though she is, and in fact actively goads the accuser into a fight. If PC-98 depictions are still considered canon, she invades the underworld, tells the Satan equivalent she did it because she was bored, and says that genocide is just a game, whether it's humans or demons. Debate rages whether she actually believes that or just said it to piss Shinki off. If asked, her answer would probably be yes.
And then there's Hijiri Byakuren who is considered frustratingly weird by both humans and youkai alike. Why? Because she treats everyone, regardless of whether they are human or youkai, with kindness and wants for mankind and youkaikind to live in peace and harmony with each other... Completely and unreasonably incomprehensible that one.
Tenshi can be thought of this, if you take into account she caused so much destruction in Scarlet Weather Rhapsody just 'cause she was bored. According to ZUN, she has a good personality and everyone were being bullies. It doesn't help any matters that she wasn't raised knowing the responsibilities of her powers.
Chrono Trigger DS's ending suggests that Schala is the reason Time Devourer desires to destroy everything, which makes it even more complicated since we can't know which part of Time Devourers' actions come from Schala and which from Lavos.
Several of the alien races in Star Control 2 have, well, alien outlooks on things:
The Orz are friendly enough with most anyone they meet, if near impossible to understand because their language is so bizarre. They seem happy to form alliances and aid in battle. They also get angry (or *frumple*, as they put it) enough to start a war if anyone talks about the Androsynth, for reasons unknown. A prominent but unproven theory is that they wiped out the Androsynth, again for reasons unknown. Then there's the fact that nobody really knows what they mean by *connecting*, *parties*, or *enjoying the sauce*. There are many hints in the story that these seemingly innocuous terms mask a sinister meaning, but that's all they are - hints. It's impossible to say for certain. They themselves seem to fall victim to this trope: when they greet the player in deep space, they state that they don't understand why *campers* (aka us) always say "hello" when they meet each other, but they do know this makes *campers* happy, so they do it too. One of the theories surrounding the Orz is that they appear like individuals to us, but are in fact a single organism existing outside our universe, alone in its own dimension. This is why the Orz creatures you meet tend to call themselves "fingers", protruding into our space from *Outside*. Orz probably doesn't understand the concept of separate individuals living in the same universe, which would lead it to assume that all the creatures it meets in our universe are just fingers of another being. Therefore, to Orz it would appear as though it has met someone whose fingers keep talking to each other, which is very odd, but they may as well play along.
"You are a *silly* *camper*. Orz is not *many bubbles*, Orz is one with many *fingers*."
This is actually reversed with the Xchaggers from Star Control 3: you meet a creature who looks like a bug with many eyes and claws, but when you talk to it you realize that it is not an individual at all but in fact a colony of billions of individuals operating together. The Xchaggers compare their workings to your own brain consisting of nerve cells, none of which by themselves are intelligent, but can function together to produce a thinking mind. Just add to that each cell having an individual personality.
The Mycon, fungal creatures with gestalt consciousness, have a unique logical operation. This stems from the fact that each Mycon shares the identity and memories of each of its ancestors. As a result, their agendas seem to span thousands or even tens-of-thousands of years, and thus their motives for any action are nigh unfathomable. At one point, if the Captain helps them locate a new world to Colony Drop, they offer to implant Mycon spores in his head to remove his individuality and make him one of them. They honestly seem to think this would be desirable. This is colored a bit by the fact that the Mycon truly are just outright insane - biological terraformers produced by the Precursors whose programming has become corrupted into a bizarre religion. This was in the dubiously canonical Star Control 3, but later Word of God confirmed that this was what the series creators intended.
The Thraddash are some combination of Blue And Orange Morality and Too Dumb to Live. When you meet them they are on their nineteenth attempt at having a civilization, having nuked themselves back to the stone age eighteen times before. They revel in combat (which would make them Proud Warrior Race Guys), but are lousy at it. They attack you without provocation, but will listen to your advice and attack much more powerful races (and be annihilated) if you beat them enough times and suggest it. They worship a piece of Precursor garbage as a sacred artifact. And if you manage to impress them, you can convince them to start a new society based around imitating classic comedians like The Three Stooges.
One of their attempts at civilization focused on criticising the cyclic life of the Thraddash, pointing out that they kept nuking themselves back to the stone-age, and maybe that wasn't such a good idea. They were (to the Thraddash) disproved by their own fall only nuking the Thraddash back to the Iron Age. Bronze age, at worst. This has gotten to the point where the Thraddash have no idea how else to make a societal change, and when the Ur-Quan conquered them, the Thraddash decided that a change was necessary... thus starting a nuclear war. The Ur-Quan took away all their nukes and gave them a warning. Not to be dissuaded, the Thraddash used chemical and biological warfare to the same effect. The Ur-Quan sternly told them that any further attempts at "cultural improvement" would be halted by the abrupt and total obliteration of the Thraddash, which finally made them behave.
The Umgah behaviour seems to be directed mainly towards gaining entertainment. They deceived the Ur-Quan into thinking the Spathi (the self-proclaimed coward species) wanted to become a Battle Thrall. Why? Because they found it amusing to force such overt cowards into combat! Then they sent subspace messages to the Chaotic Evil Ilwrathi pretending to be their gods, and goaded them to fight who they thought would be a fun foe. When you meet the Umgah in Star Control 2, they are initially all under telepathic control by a single mentally powerful creature. When you free them from that, they praise you as their hero, and hand over a few of their battleships to your fleet. Then they decide during the same conversation that you being their great hero is boring, and having you as their great enemy is much more exciting! And then they attack you.
The Qunari of Dragon Age: Origins. On the surface, they're just a Proud Warrior Race with a proactive magic phobia (considering the way magic works, that's actually a smart mindset), but the more you talk to Sten, the more they start to evoke this trope. According to Sten (the only Qunari we interact with in the main game), your career is as much a part of you as your skin color or gender. Their occupation is given at birth, the same as their soul or consciousness (there's some evidence that they may view all three as one and the same). The Qun (qunari religion) is built around the idea that you have only one important choice: you can choose to play your role, or die. They don't see this as a contradiction — as far as they're concerned, merely existing proves that you choose to live, and to live is to follow your role. In camp, Sten spends most of his time talking to your war dog, since he can relate to him best - the dog, after all, has a role which he performs admirably, and never questions or seems to desire any other. To Sten he may well be the least alien of your party due to this fact. To the Qunari, even your gender defines what you can and can't do. The word warrior is synonymous with male, while the word manager is synonymous with female. They simply don't understand the concept of a woman who fights. This can lead to Sten deciding a female PC is not in fact, a woman. "I don't understand. You look like a woman." For extra intrigue, when most members of your party will oppose some of your decisions because they have ethical or practical objections, Sten will protest because you are stepping outside of your role as a Grey Warden, which is to end the Blight and nothing else. And if he raises his doubts about what you are doing and you tell him to stop contradicting you and fall in line, he will approve.
Morrigan has shades of this as well. Despite voicing a Grey and Black Morality loudly, she has never met or interacted with anyone but her mother for long, and may end up at this moral state by the conclusion of her DLC.
The Architect shown first in the novel The Calling and then in Dragon Age: Origins – Awakening shows this. He's a sapient Darkspawn, who has decided he wants to end the Blights and the fighting between Darkspawn and the other races. Unfortunately he clearly has no understanding of the sensibilities and morality of non-Darkspawn, and thus its original plan for ending the Blights is rather horrific and would result in the deaths of large numbers of people. He has no idea why people would object to this since it would end the Blights that have killed many more people. Fortunately by the time of Awakening he's come up with a somewhat less horrifying plan though he still doesn't get morality and still does some pretty nasty things just because he doesn't understand that they are in fact bad. He feels bad for not understanding since he knows it hinders his ability to achieve his goal of peace.
In Dragon Age II more insight into the Qun is gained as people actively try to push the Qunari too far in order to spark a conflict. Eventually, The Arishok becomes so sick of what he sees as the lack of morals and principles that he feels define organisms that he starts a war.
Hawke: I see a man willing to start a war on principle.
It doesn't help that they often refuse to talk about their beliefs, thus perpetuating the ignorance. And then take violent actions that more often than not make no moral or ethical sense to anyone but themselves. As far as they're concerned, it's either all self-evident, or it is not their role to explain it to you, and therefore they cannot. Talking about it to them just proves to them that you don't get it. They don't care what your race is, though. Anyone who freely chooses to follow the Qun is considered one of their own and will be treated as such. Even if those who chose to follow the Qun are merely doing it to get their Qunari's protection.
A different example of this is Anders, who is possessed by the Spirit of Justice, now transformed into a Demon of Vengeance due to Anders' hatred of the circumstances that resulted in the creation of the Circles and the oppression of mages. Justice/Vengeance isn't human, but rather a spiritual entity devoted entirely to that concept, and he and Anders are so integrated that Anders isn't sure where his mind ends and Vengeance begins any more. As the game progresses, Anders becomes more and more unreasonable and dogmatic to the point where it becomes questionable whether or not Anders is being driven by human morality at all.
Of course, the perception of Anders as "unreasonable and dogmatic" is also an example of this trope depending on the player, for Anders' behavior is actually understandable if you start from the premise that people have human rights, including the right to "exercising power over their lives", rather than being treated as though they should accept treatment whatever they get. Following from that premise, Anders is right to passionately fight for a group that has had its rights taken away and can get no sympathy from anyone. If you don't start from the premise that people have rights; if instead you start from the premise that the primary job of people is not to "bother" each other with their cries of pain, then Anders' behavior is incomprehensible and confusing. After all, compared to everyone else's suffering, a few mages being locked up doesn't really matter in the grand scheme of things.
And Justice counts before his corruption into Vengeance. He/it is not a human but a spirit who personifies a single concept - justice - and therefore doesn't adhere to the same morality as mortals. He can only think and see within the constraints of what is just (in Awakening, he believes Anders is enslaving his pet cat). The same can apply to all spirits/demons, who latch onto a single facet of human emotion to anchor themselves in the chaos of the Fade; it's theorised in the game that spirits who enter the human world are almost always hostile because they don't understand how to cope with a world that isn't constantly in flux, and therefore constantly lash out in fear or confusion or find a mortal host so they can forcibly gain the understanding.
In World of Warcraft, a great number of forces simply see mortals as plants in the Titans' garden, to be pulled or fertilized as the situation warrants.
Algalon the Observer rightfully sees that the Old Gods haven't been properly contained and has decided to "re-originate" the planet.
A common interpretation of the war between the Blue and Red dragonflights is that neither is good or evil, the former is simply trying to do its job (guarding magic) by killing all mortal magicians, and the latter is just trying to do its job (guarding life) by saving them.** To provide more insight into this in Warcraft lore magic is responsible for (or aided in allowing) numerous bad things to occur, like an Orc invasion, the Orc homeworld blowing up, a Demon invasion, a Zombie invasion and more notable the Sundering that tore apart and created the various land masses of Azeroth.
Elementals are like this quite often, as they are considered purely chaotic. One water elemental, Duke Hydraxis, notes that he does not understand the human concept of gratitude or giving rewards, but in accordance with it, gives you a special item as a reward for a (now removed) quest.
In the fourth expansion, we have the Mantid, whose entire society/cultural system is based on the cycle of the swarm. Every 100 years or so, their young hatch in incredible numbers and then swarm toward the rest of Pandaria, devouring anything in their path. The Mogu, got Genre Savvy on this and built (using slave labor) the Serpent's Spine, a Great Wall of china expy, to better defend Pandaria from these periodical attacks. Still Mantid assaults on the Serpent's Spine see the genocidal war between mantid and defenders (first Mogu, then after their revolution Pandarens took that role), which inflict heavy casualties on the defenders before being forced to retreat for arguably taking several times those losses on their own forces. Mantids who survive this make their way back to their tree cities, bearing trophies of their conquests and take their place among their civilization according to the level of their deeds. These practices pretty much assures that the mantid who survive into adulthood are adept warriors in whatever areatheychoose tospecializein. The kicker, they do all this as a form of worship to one of the Old Gods, their "master", with the ominous implication they will use the evolved warriors/tactics/technologies they get from this social Darwinist system to kill or worse all the other races should their God ever come back. Even worse, the majority of their race has been corrupted by the Sha of Fear, who have skipped the whole waiting for our god to return and went straight to zerg rushPandaria.
Also from the fourth expansion, another villain race, the Mogu, have a pretty distinguishable motivation, which also seems to be an in-universe example of motive decay, since the founder of their empire, the Thunder King Lei Shen had another justification, which seems to be a mixture of "Well Done, Son" Guy and Gone Horribly Wrong, for enslaving other races and building his empire through unholy means. The exploration slide show (called, appropriately, Gods and Monsters) says it best:
The Einst from various Super Robot Wars games exist for the sole purpose of preserving the universe(s). Since human consciousness is slowly causing the entropy of existence, that means mankind has to go. However, for unspecified reasons, they've decided that simply wiping out humanity won't do, and they decide to replace it with a new human race that lacks souls and emotions, and is no longer a threat. Unfortunately, one of their owndidn't think it could work.
The Strogg, the main villains of the Quake series, turn out to be motivated not by a desire for conquest, but survival, as capturing humans and "Stroggifying" them is how they reproduce.
Almost every powerful entity in the Shin Megami Tensei series operates under this; to the point where there are basically only one that is actually good (Philemon) and one that's actually evil (Nyarlathotep) by our understanding (and even Phil has severe issues with his chosen champions). All the others have mindsets so alien that trying to call them good or evil is a waste of time; as they don't think anything like humans. Yes, even YHVH. Bear note that the alignment system isn't good-evil, law-chaos, but law-chaos, light-dark, with the latter determining how far from the ideals of YHVH you are - the fallen angels are dark exactly because they were cast out for disagreeing with YHVH, and YHVH is perfectly light because He marks the starting point of the scale, morality notwithstanding. Even Erebus is debatable — as explained in The Answer, he's only destroying the world because so many people secretly long for death.
This is even something of a mechanic when it comes to negotiating with demons, who sometimes can be won over with pretty "human" means by being kind, flattering, sucking up to, or outright bribing them, but other times some demons respond positively to being threatened, obviously lied to, or praising bloodshed and destruction.
The blue and orange morality of demons is also a plot point in Strange Journey, where the demons apparently believe they're doing captured humans a favor with their "experiments," which invariably involve killing people by removing their vital organs. According to notes, the demons are convinced they're freeing the humans from their worldly cares and needs. This contrasts against what one faction of humans do later in the game, capturing and mutilating or killing demons, but just out of greed.
The Big Bad of Persona 4 genuinely wants to make the world a better place to live in for humanity. However, she has a very limited understanding of humans and what they really want. She ended up decided that the best example of a human being was a psychopathic Serial Killer, simply because he was the best at leading people from a certain point of view. As such, she paid attention to his very skewed perception of people, and determined that the best way to make a paradise for humanity is to make an Assimilation Plot. Thankfully, she's reasonable enough to admit she's wrong when you defeat him and her in turn; once the fight's over, she agrees to leave humanity alone until she has a better understanding of what exactly is going on.
Crysis hints at this with the Ceph, but the novelizationCrysis: Legion all but outright says that the Ceph have an alien morality. Hargreave presents a theory that the Ceph are "gardeners" who awoke to find humanity messing up the biosphere they created and are removing an infestation (human attempts to understand the Ceph, he argues, are equivalent to locusts trying to understand human attempts to exterminate them) while Alcatraz/Prophet theorizes that the Ceph are not the gardeners, but the tools of the gardeners left behind to activate and fend for themselves. A CIA analyst at the end of the book proposes a third theory, that the Ceph's technology and motivations are completely beyond human understanding, and that the entire "invasion" was an effort to recover technology like the Nanosuit that Hargreave invented based on Ceph tech.
Dwarf Fortress has elves, who find it unthinkable to kill plants, but are perfectly okay with eating the corpses of their enemies. The game also has a set of ethics parameters that are quite easy to modify, making it simple to create a race or modify an existing one with strange moral values. Heck, even the DF player community can fall into this at times, as they frequently consider Video Game Cruelty Potential not just amusing but a mandatory part of gameplay; if you don't start gleefully butchering kittens and building giant doomsday devices out of their bones to slaughter your enemies (or dwarven nobility) at some point, you're an alarming aberration and likely to be accused of being an elf in disguise.
The Brothers of Turgor seem to have a very strange morality from a human perspective.
Triumphator: Giving is an unquestionable evil, so taking must be an unquestionable good!
The Shivans of Freespace have a morality that is completely incomprehensible to humanity, or indeed any to other being who's ever encountered them. This is because the Shivans do not communicate, indeed do not even try to communicate: They simply kill all non-Shivans with subspace technology on sight, and then hunt down the rest of their species down to the last man and exterminate them all. Nobody knows why they do this.
It gets even more strange in the sequel, with the Shivans looking set to do the above and the GTVA desperately working to seal the entry point into the rest of GTVA space... and then the Shivans make a star go supernova. There is some theorizing in the outro about why, but nothing is confirmed and it doesn't have any apparent connection to hunting down species with subspace technology.
Another unexplained action they take in the second game is kidnapping Admiral Bosch and his command staff alive when they finally managed to get a communication across to the Shivans. This is completely outside their usual MO and has confused many a fan of the series.
Capsuleer motives are seen as this by planet-dwellers in EVE Online. It doesn't help that even among the various capsuleer factions there's a general theme of sociopathy with rules unique to each group.
The Think Tank scientists from the Fallout: New Vegas add-on Old World Blues. While they created amazing and beneficial technologies like replicators that could have averted the Great War and cyborg implants, they are also responsible for 'lobotomizing' innocent people into mindless slaves and the deadly toxin called 'The Cloud' that still kills and mutates people even 200 years later. They don't care about (or deny or regret) the horrifying repercussions of their actions because the experimental data is yet another step in the glorious cause that is SCIENCE! Also, the Think Tank have spent the past 200 years as Brains in Jars, so they have long since forgotten what being human is like. To wit, they initially they all believe that the Player Character's fingers are penises, and the token female of their group is fascinated by the Player Character's breathing to the point of becoming sexually aroused by it. This aspect of their deteriorating frame of mind is Played for Laughs, of course.
From the previous Fallout game, Fallout 3, we have Charon. Charon is a shotgun-toting ghoul merc with a mysterious past, currently in the service of Ahzrukal. He was brainwashed as a child to follow whoever holds a signed piece of paper, his "contract". While Charon is fundamentally good-ish on his own, he gives Undying Loyalty to his contract-holder and will do anything his contract-holder tells him, without question or hesitation, no matter how morally reprehensible. Once freed from his contract, however, he has zero qualms about turning on his former master, as Ahzrukal or potentially an evil Vault Dweller finds out.
Sometimes, even Griefers have standards - some Griefers only engage in Griefer-like activity simply because it's funny. They may thrive off of Chaos, but they don't find it very funny when people are actually hurt or Second Life servers crash. Sometimes, a Griefer may actually be intentionally trying to come up with whatever crazy stuff they can find specifically to test-out anti-griefer measures on servers; or the server stability in the event that a real Griefer comes in with intent to destroy. One Second Life sim actually encourages people to attempt to crash it, and if they do, they try to find out why it crashed so that they can help create more stable servers in the future. There are also sometimes where people come in to try to be funny just cause well, it's funny!
For that matter, a lot of "Chaos"-types. Some people thrive off of the chaos, but only if people are around to appreciate the chaos and the insanity.
From Pokémon Black 2 and White 2, Colress. He doesn't consider the morality and consequences of his actions, just the results and knowledge that can be gathered from them.
Haer'Dalis from Baldur's Gate II is remarkably natural in following the alien philosophy of the Doomguard, perhaps more so than most of its adherents. He's basically a balanced nice guy who wants to see the world burn — not by causing it, at least necessarily, but watching it fall apart by itself, which he sees as more exciting than regrettable. He's passionate about things but does not desire for them to last, treating everything more like a fleeting artistic performance ending in destruction. Though Chaotic Neutral, he can win the love of the Lawful Good Aerie, only to have her leave him later when she sees the difference in the ways in which they care about things — and each other.
The Wisps (AKA Xorinites) in the Ultima series have what seems like an askew morality to humans. It revolves around the acquisition and application of information. In the first discussion you have with them in Ultima VI, they casually hand you a spell which destroys all life in the entire world around you. Why? They consider such a thing completely useless (presumably because it eradicates countless sources of information) as well as not being very powerful (since it can only eradicate life in one plane of existence), and they wish to teach you a lesson that not all information is valuable. Later in Ultima VII you need to bargain with the Wisps as part of the main plot. Specifically, they task you with acquiring for them the notebook of a scholar who is investigating the game's Big Bad. Right after you do that, they sell this information for the Big Bad in question, who proceeds to have the scholar killed. Still, it's hard to get mad at them.
In the sixth game, you can sell the contents of a rather dry reference book (not the book itself, they just copy the contents) in exchange for "a small amount of precious metal", meaning all the gold your party can carry. They will at first assume you'd prefer information of comparable value rather than a bunch of Worthless Yellow Rocks and offer to renegotiate, and are surprised when you say you're okay with the deal. (If you do accept information, you'll get a scientific principle that could very well be priceless to a scientist, but not a sword-wielding fantasy hero.)
Zagara has a peculiar musing at one point on human individuality. She seems to think that being individuals would make all humans "extremely lonely", and thinks assimilating them into the Swarm would not just be useful for the Swarm, but would actually make the assimilated humans happier. Kerrigan (the only human to have ever been infested and retain her own personality) disagrees.
But the most egregious example of this trope in the game has to be Abathur, a weird mixture of For Science!, Evilutionary Biologist and Mad Scientist. Some of his quotes might shed some light on his morality, but do notice the odd speech pattern, often leaving out words, presumably because it's a more "efficient" way to talk:
Abathur (about his job): Look at flesh, see only potential. Strands, sequences, twisting, separating, joining. See how it could be better. Make it great. Abathur (about creating perfect beings): Never perfect. Perfection goal that changes. Never stops moving. Can chase, cannot catch. Abathur (about increasing zerg intelligence/individuality): Extraneous brain matter deemed unnecessary for broodmother role in Swarm. Extra matter requires extra energy. Also leads to increased independence. This contradicts imperative: zerg must present no danger to leader of Swarm. Abathur (comparing primal zerg and normal zerg): Primal Zerg. Dynamic. Varied. Messy. Reactionary. Improvised. Unsuccessful. Some good sequences, can steal. Swarm efficient. Careful improvements. Successful. Abathur (about Zerg evolution under Kerrigan): Queen determines purpose. When purpose changes. Swarm changes. This our function. Abathur (about Kerrigan's suggestion to put failed experiments out of their misery): Wasted effort. Creatures will die soon. Pain irrelevant. Abathur(When told by Kerrigan that she's warming up to him): Unclear.
Halo: The Hunters are known to be Punch Clock Villains, but their true motivations are known to them alone. They intentionally reinforce this image so that the other races of the Covenant will leave them alone.
The Gravemind has this for the Flood. It seems to think that all beings being absorbed into the Flood is perfectly natural, and cannot understand why people fight against it. Some of lines reflect this:
"Do I take life, or give it? Who is victim, who is foe?"
"Resignation is my virtue, like water I ebb and flow. Defeat is merely the addition of time to a sentence I never deserved, but you imposed."
The Forerunner Trilogy manages to simultaneously play this straight and subvert it. The Flood is the reincarnation of immeasurably old and unimaginably powerful beings known as The Precursors. On one hand they are every bit as inscrutable as beings that old would be. On the other hand the Flood has a very clear purpose, revenge for the Forerunners nearly wiping them out.
The "Dragonfall" DLC for Shadowrun Returns features an AI who claims to that concepts of "good" and "evil" are human judgments irrelevant to it.
Every NPC in Gingiva has a very bizarre perspective on just about everything, which is very appropriate for the surreal Mind Screw theme of the game.