In the Mahora Fest arc, Negi and his allies are unsure of whether they should allow the masquerade to be permanently broken. The boy eventually just accepts that he might be the villain in this case but decides to stop Chao either way, because she doesn't give him a good reason why he should let her continue. Later events, though, show unambiguously that Chao could've improved on the actual outcome if allowed to win. The risk of corruption and her constant downplaying of her intentions, however, ultimately influenced Negi to decide to fight for the present rather than look to an unknowable future.
In the Mundus Magicus arc, it is revealed that all Fate wanted was to save Mundus Magicus... except his method risks lots of collateral damage (specifically, the Artificial Humans that comprise majority of its population). Simply put, Negi and Fate are basically fighting over who can do a better job of saving it.
Tower of God: Sure, one could say that the people who betray and manipulate are the worst guys, but every single one of them has reasons that make then Not So Different. At the same time, the protagonists have to constantly crush the dreams of other people to advance. One could say that the black would be the system with it's inherent injustice, but then one would have to concede that the great conspiracy in the back ground has a noble cause. Also, the system has increased the chances of achieving ones dreams by several powers of ten, and many of it's members are pretty nice guys.
To a lesser extent, the ambitions of the Big Bad in the obscure video game Slayers Wonderful can be interpreted as this, as the scientist Viola (the antagonist) wishes to seal magic in order to stop the warring between humans and those above them. Once again, though, it shows A Lighter Shade of Grey.
Gundam has made a point of this trope since the original series. Although the antagonists, Zeon, are generally seen as more evil than the Federation, Zeon's causus belli are understandable and realistic, while the Federation commits its fair share of atrocities across the series as well. In the end, no one side can claim to be exclusively good or evil.
Gundam Wing started off with the heroic Colonies rebelling against the evil Alliance and later OZ, but by the end, it was really hard to tell which side we were supposed to be rooting for. Ultimately Treize and Zechs (and a few others from OZ) are just as heroic as the Gundam pilots, even if their ideas clash; it's the Manipulative Bastards such as Quinze and Dekim who are considered the true "villains".
Mobile Suit Gundam 00 started out with Celestial Being more or less trying to force the world into peace. Unlike most Gundam series, none of the major power blocs are that corrupt or violent. However, in the second season, the various sides of the conflict become much more black-and-white, as the Gundam pilots started acting on freewill and the world seemingly uniting under the The Federation, which being deconstructed, has suddenly become much more evil, despite containing many of the sympathetic antagonists of the first season. Its sudden turn to villainy is ultimately revealed to be the machination of the Innovators, led by one madman with an outsized ego.
Noir, despite its name, actually isn'tBlack and Gray; it's fairly dark, but it's more like slate and charcoal than anything else.
Darker Than Black. Amber's organization, Evening Primrose, wants to seal off Hell's Gate to prevent The Syndicate from destroying it, thereby wiping out every Contractor in existence but also Japan. Hei is actually working for said syndicate throughout most of the series, as are most of the people who get in his way, since they're keeping the Contractors busy fighting each other unless they discover their superiors' real goal. Plus everyone's a Punch Clock Villain.
In the end, Evening Primrose landed in more white territory — when they found out that there is a third option in which neither Contractors nor Japan are destroyed, they went for it.
Simoun, from the beginning. It starts with the POV of someone from one of the peripheral, heavily polluted nations talking about why they are invading Simulacrum, and it has examples throughout of both sides doing good and bad.
Steamboy explores the relationship between mankind and science, and aside from the O'Hara Foundation proper, none of the sides (Eddie Steam, Lloyd Steam, Scarlett O'Hara and Robert Stephenson) are shown to be entirely right or wrong.
Vinland Saga is about vikings. The main character could generously be called a Sociopathic Hero and doesn't actually care what side he's on. The sides in question change, merge, and are destroyed through various slaughters and assassinations. It isn't so much this as Gray Stew.
The exceptions on both sides are Kurama and Nana who would rather avoid any more pain and death, but they are about the two most messed up characters in a story where every single person has serious problems with their mental health (and There Are No Therapists).
Heroic Age at first glance appears to employ Black and White Morality between the human protagonists and alien antagonists, but it eventually goes on to show some humans Kick the Dog a few times, while some aliens are portrayed sympathetically and others afraid that humans will kill them unless they Kill All Humans first, while both races appear to suffer from Blue and Orange Morality. Eventually, this trope is lampshaded and taken to its logical conclusion when both sides call a truce and eventually end the war.
In Neon Genesis Evangelion, opponents NERV/SEELE and the Angels have a common goal: destroy the opponent and initiate Third Impact for their own ends. Eventually, NERV and SEELE oppose each other as well, since they have one slight difference in what do they want to do with the Assimilation Plot.
Although Nabari No Ou initially appears to be a case of Black and White Morality, it's actually one of the rare cases where both sides are portrayed as more or less equally good — There's an equal number of heroes and villains on each side, and most of them change sides at least once. In the end, it turns out that Fuuma and Hattori have been working together all along.
Revolutionary Girl Utena is a perfect example. The student council are all fighting for their own personal goals (none of which are truly good or bad), and this applies to most every other character. Even Utena herself falls into this through most of the story, fighting because she wants to be a prince, and struggling to find her identity amongst it all rather than out of a sense of justice or love.
Desert Punk definitely fits this. Initially, it's a case of Punk fighting against people who are not much worse than him (and occasionally are somewhat better), but the ultimate plot about a rebellion falls squarely into this too. The Oasis Government presides over a horribly inequitable system (which is partly Inherent in the System because of the wasteland setting) and is involved in various conspiracies to control Lost Technology and silence those who find out about it. The rebels initially seem to be A Lighter Shade of Grey, especially since sympathetic and idealistic government officials join them, but are made morally ambiguous because of a Utopia Justifies the Means attitude, which includes hiring unpleasant, even villainous characters to help their cause, one of whom has the outlook of an Omnicidal Maniac and is just manipulating them to advance his own goals.
Given Real Life history, the Moe Anthropomorphisms of the various nations in Axis Powers Hetalia are definitely this. As everyone's shown to be good-at-heart in their own ways, not one of them is portrayed as utterly evil, including Ivan/Russia. And if they're given enough time in the spotlight, almost every country is revealed to have a few jerkass traits.
In the second half, Autozam, Chizeta and Fahren meant well even while invading Cephiro to make its leaders become Pillars — Eagle wanted to clean his polluted planet but also to put Cephiro and himself to sleep to avert another Pillar crisis, fearing his best friend Lantis will kill himself trying to destroy it; Tarta and Tatra wanted to relieve Chizeta's population pressure; and Princess Aska only wanted it for fun until Fuu convinced her to be more mature with what she really wanted in life. None of them wanted to deliberately do evil, yet each one had goals that would have eventually hurt others. In the end all three make their peace both with Cephiro and each other. The only unambiguously evil character throughout the series is anime-exclusive Lady Debonair — who is nothing more but the personification of Cephiro's despair following Emeraude's death.
Getter Robo villains are at best Anti-Villains, at worst Well Intentioned Extremists. The only villains that crossed the line are human, and really, it's hard too see how the villains are "evil" especially in the manga when most of them consist of the villain fighting for the happiness of their people, or trying to save the world, complete with several Heroic Sacrifice to save the world. The only explanation for their status as villains are the fact that they are not human.
The feuding ninja clans of Basilisk are equally honorable and treacherous. As are the heirs' nannies who instigated the contests with their own intrigues. The Treacherous Advisor/Big Bad wasn't in support of either side so much as conflict for the sake of pain and misery. In that sense, even though defeated, he won in the end.
Karakuridouji Ultimo might as well be called Grey and Gray Morality: The Series. The incarnation of Ultimate Good murders the main character's princess wife in a fit of Black and White Insanity, and that doesn't even begin to scratch the surface.
Maoyuu Maou Yuusha deconstructs the Black and White Morality prevalent in many other fantasy works when the Demon Queen reveals the truth to the Hero about the human-demon conflict: neither side are wholly good or evil, just the individuals and their actions. On one hand, the war helped unite feuding kingdoms against a common enemy. On the other hand, opportunists came in to exploit civilians and get rich off the war. Both the Demon Queen and the Hero, who can pride themselves of A Lighter Shade of Grey, now set off to cut through the war and find a more peaceful solution.
Applies to nearly every character and situation in A Cruel God Reigns. Does Jeremy kill his stepfather or does he continue to let himself be abused? How should Ian feel about Jeremy- does he forgive him or does he hate him for murdering his father? Is he in love with him or does he just want to atone? The series revolves around those two issues, but nearly every character has some situation like this at some point in the series. Not only are their situations Grey and Gray as well as Black and Gray Morality, but the way the characters deal with these situations is often muddled in good and bad.
The fight between both gangs in Yukine's arc of CLANNADAfter Story fits this trope. Although it is never made particularly clear what the motives of both sides were, Yukine was willing to assist and nurse both sides, despite the fact that the leader of one gang was her belated brother.
In Blade of the Immortal it's hard to know who to root for sometimes, since the vast majority of the cast, even if they engage in questionable behavior (the so-called "villains" frequently moreso) usually have something understandable that they are fighting for and show that they are fundamentally decent people; most of the conflict in the series is merely due to someone's interests interfering in another's. There are a handful of exceptions, notably Shira, who is completely irredeemable.
Death Note is this way for sure; LightYagami is a homicidal Villain Protagonist who kills criminals on a global scale, along with anyone who gets in the way of his mission; L is a coldly logic-driven Sympathetic Inspector Antagonist whose investigation methods include befriending serial killers and Cold-Blooded Torture. Both of them, however, have the same basic goal: to defeat what they see as evil. You can hardly blame them for that, even if their methods are more than questionable.
K: Across from the Colorless King and a few unambiguously good characters, none of the characters are portrayed to be entirely good nor evil. Specific mention to the conflict between HOMRA and Scepter 4 clan, which falls more into the lines of Order Versus Chaos where both clans have their own set code of morals. The HOMRA clan functions more like a ruthless street gang and will go on a violent Roaring Rampage of Revenge if any of their members are killed, but they have a strong sense of camaraderie where members treat each other as a family. Likewise, Scepter 4 functions like an elite police force who have strong ties to many police departments and the Japanese government and is willing to maintain the peace, security, and prosperity of Japan, but they lack the sense of camaraderie that HOMRA has. Also, note that there are some clan members from Scepter 4 and HOMRA have some form of Friendly Enemy relationship and even have to work together to evacuate the Ashinaka High School students so Adolf K. Weissman can safely defeat the Colorless King.
Mother Keeper has this, on one side the people in the slums are rebelling because according to them Eden has ruined their lives and left them in a terrible condition. On the other hand, Eden says they've done nothing to these people and claim that they're just a bunch of terrorists attacking for no reason. Even the main character has reached a point where he doesn't really know who's side he should be on.
IDW's Megatron: Origin miniseries shows the series's iconic Evil Overlord's rise to power from a laid-off energon miner through underground gladiator to the leader of a rebellion against a corrupt Cybertronian senate, with the Autobot Security Services presented as an incompetent and in some cases fascistic police force under the control of the aforementioned senate.
Before this the Dreamwave comic series revealed that the Autobot ruling council were servants of the Quintessons, the Transformers' entire history was a lie told to keep the Autobots in line and Megatron, having found all this out, forced the Decepticons to try and free his people and to bring order to the universe, albeit through very Knight Templar behavior.
World War Hulk: Warbound vs The Illuminati. The Illuminati weren't guilty of the crime that Hulk was avenging, but they were the reason he was on Sakaar in the first place.
Superman: Red Son: Superman is a totalitarian dictator who brainwashes any domestic political threat including Batman, but values human life enough to never kill anybody and - to himself, at least - has humanity's best interests at heart, while Lex Luthor is totally obsessed with bringing Superman down rather than liberating humanity from Superman's yoke but does so by attempting to prove that he is the better leader. In other words, in this story, Superman's intentions are good but his means are evil, whereas Luthor's is the other way around.
Dungeon Keeper Ami is a highly unusual example, being something of a crossover-Fusion fic combo. What's interesting is that Grey-and-Grey is played straight, inverted, averted, and sometimes double-inverted. Sometimes all at the same time. This is accomplished by having the titular heroine and the current universe she resides in both play Black and White Morality very straight, but the heroine herself is bonded to an undoubtedly evil artifact. The forces of good, unused to such a situation, are reluctant to consider Ami as anything not-evil. The forces of evil consider her either an abomination, or the most brilliant case of evil overlording gone right.
Tiberium Wars portrays both the Global Defense Initiative and the Brotherhood of Nod in sympathetic light, with Nod being presented as desperate and angry and vengeful for the wrongs GDI has perpetuated on them, and GDI being presented as Well Intentioned Extremists who nonetheless are trying to protect the world and defend themselves against Nod aggression.
It should come as no surprise, but the crossover fanfic Renegade by the same author does the same thing, with the same factions. In fact, both factions are presented as protagonists, with the Brotherhood of Nod intervening in the slaver raid on Elysium and with Kane himself attempting to negotiate a compromise between GDI and the Citadel. Of course, Nod apparently stole the Tacitus on Eden Prime, which caused said conflict between GDI and the Citadel and allowed Kane to score points by negotiating said compromise, so it might have been part of the plan....
Fittingly, considering the canon series' Grey and Gray Morality and Black and Gray Morality tendencies, the Mass Effect fanfic The Council Era is entirely these two. The Villain Protagonist seeks to create a Utopia for the galaxy, and does improve it over time, but he believes that Utopia Justifies the Means and commits seriously heinous acts in order to marginally improve the galaxy. His Worthy Opponent in this Evil Versus Evil plotline merely seeks to create a firm foothold for his newly spacefaring people, the krogans. By exterminating every other species, and turning the krogan into a Master Race.
24: The Musical, a fan-made musical of 24's second season lampshades this in the song "Dammit!" Jack Bauer sings that "Sometimes the rules can be gray," in justifying shooting Marshall Goren and then asking for a hacksaw.
Jack: Get me a hacksaw, cut off his head!
Mason: Are you crazy, Jack?
Jack: Come on, George. He's already dead! I know this is drastic, it's all that we've got. Sometimes the rules can be gray!
The Conversion Bureau. The ponies are fairly consistently portrayed as racist (speciesist?) to varying degrees, but genuinely believe that their actions are helping humanity and leaving them happier in the long run. Humanity is only trying to defend itself, its culture, and its world but seems to take rather perverse glee in living down to its thuggish reputation in the process.
The Angels themselves aren't the only reason the Federation is gray. The Muslims of the Emirate of Mecca - one of the founding Federation states - are a totalitarian theocracy that use suicide bombers as their main weapon and do very unpleasantthings to their women to increase their numbers. The Jews of the Tribal Republic/Diaspora Fleets are technologically backward primitives who fight among themselves and the Muslims more than they fight the Demons.
In The Fairly OddParents fanfiction, Never Had A Friend Like Me, this is how Norm sees the genies vs. fairies arrangement. Norm has declared many times that he gets a kick out of tormenting masters by screwing them over, but he at least he doesn't pretend to be a saint. And while fairies do enjoy having godchildren and try to fill the gap their parents can't, he thinks the fact that fairies eventually terminate their relationships with their godchildren, not to mention their memories of time together is also pretty cruel. Granted he may have a point, considering Amanda his current master, and the most selfless girl he's ever encountered, is pretty horrified by the concept.
The concept of portraying evil and then destroying it - I know this is considered mainstream, but I think it is rotten. This idea that whenever something evil happens someone particular can be blamed and punished for it, in life and in politics is hopeless.
Though Studio Ghibli films usually tend a bit more towards White and Grey Morality, this is generally true. Princess Mononoke is one of the best examples (with the two sides having both good and bad qualities), and Spirited Away protagonist Chihiro is prone to the fallibilities of being a child rather than a perfect angel. It's nonetheless worth noting that Miyazaki's earlier films were more Black and White Morality, so retroactively even the writer developed a better understanding of this trope's existence.
The Matrix sequels and supplementary materials retconned the human/machine war into this, with the robots repeatedly trying to settle matters diplomatically, and the humans revealed to be lazy, arrogant, and decadent as the result of robot labor relieving much of their previous responsibility. Fortunately, peace is borne once more when Neo makes a truce with the machines to stop Agent Smith from destroying everything, thereby uniting humans, machines, programs, etc. once more.
While the Clone Wars saw the Separatists being led by a bunch of corrupt corporate executives and Sith Lords and a homicidal cyborg, a lot of the worlds joining them were only doing so to oppose what they with some justification saw as a corrupt Republic. To grey out the other side further, as Anakin Skywalker observed, even the Jedi Council was feeling compelled to move into a more pragmatic and less moral direction. Ultimately, though, Anakin's protestations about such morality when he has fallen to the Dark Side are ironically empty, as he has chosen to join with the altogether blackBig Bad who was behind it all from the start and who makes him eat kittens. Still, it should be mentioned that the Separatists are still on the darker end. Yes, the Republic ended up becoming the Empire, but the conduct of clone troopers before Order 66 was much better than the droids. Also, contrast the Jedi Generals with General Grievous, and consider the fact that many Republic generals and statesmen later became rebels. Furthermore, that corruption in the Republic? It largely originated from those same Corrupt Corporate Executives that led the Separatists. The Republic isn't perfect, but at least they don't have a reputation of wanton brutality.
In the 2007 Chinese film, Warlords, the three main characters are all grey, and so are pretty much all the characters. There are no heroes or outright monsters. This is a film that challenges the viewer to decide which is the more moral choice. Sometimes the moral thing to do results in greater harm or loss of life than the socially reprehensible thing to do.
King Kong, especially the Peter Jackson remake. Kong, an aggressive animal who kidnaps a human but wants to protect her as well, fights first a film crew — greedy, but they don't initially want to hurt anyone and only capture him as a last resort, and later the army, who want only to defend their city.
The Chinese/Korean coproduction Musa The Warrior shows both sides of the conflict (exiled Korean soldiers and defeated Mongol horsemen) to be somewhat sympathetic but deeply flawed people bound by both grim necessity and inflexible ethical codes to slaughter each other in a series of running battles which ultimately achieve little but tragic attrition.
In Election, Tracy is a sweet but borderline psychotic overachiever who tears down Paul's posters in a fit of rage, Paul is a well-intentioned but fairly clueless guy who's only running because he was told to by his teacher, Tammy is only in the race to get revenge against Paul and Lisa, and Mr. McAllister cheats on his wife and rigs the ballots to deny Tracy the victory. None of them are particularly "good," but all of them have their reasons for behaving the way that they do. The original novel is even grayer. Tracy's sociopathy and Paul's ditziness were greatly increased from their original characterizations, and Mr. McAllister's buffoonishness was a detail Alexander Payne, who wrote and directed the film, invented from scratch, purely for the sake of having a buffoonish protagonist. In the book, the characters feel more realistic and believable, making it that much easier for the reader to understand and side with them.
Inception is a curious example in that it has neither heroes nor villains. Fisher, despite inheriting a major corporation, is an innocent; Saito is a business rival of his; and Cobb and the team are only in it for themselves (Cobb in hopes of getting home to his family, Ariadne for thrills, the others for money). The antagonist, Mal, is, in the dreams, a manifestation of Cobb's self-destructive subconscious with no free will of her own.
In Air America, there are definitely good guys and bad guys, but none of the good guys are pure white-hats, not even Billy Covington and Corinne Landreaux, who probably come closest, and none of the villains are pure black-hats, not even Major Lemond and General Soong. Yes, granted, Soong, Lemond, and Lemond's assistant Rob Diehl are drug runners, but there is no evidence that Lemond and Diehl are enriching themselves, and even Gene Ryack, who is more or less neutral for most of the film, points out that it is impossible to win a war in Southeast Asia without controlling the opiate trade, so Lemond and Diehl, and even Soong, are just doing what is necessary for the war effort. Ryack himself is a gun runner, and it is made clear that pretty much all the pilots are running illegal scams on the side. Corinne, again, might seem closest to being a pure white-hat, but she's dating Rob, one of the villains. Senator Davenport turns out to be a good guy at the end, but he's willing to look the other way at Gen. Soong's rather dodgy "recruitment" techniques. So all in all, no one in the film really seems all good or all evil.
Blade Runner was certainly an example of this. On one hand, you've got the murderous replicants who simply want to be human, and on the other you have the people who hunt them to keep the streets safe who aren't entirely saints themselves.
In Now You See Me, the Horsemen are smug jerks and thieves, but they're stealing from bad people. The only main characters who stand out as good guys are Dylan Rhodes and Alma Vargas. Dylan ends up being the fifth Horseman and Alma is complicit when she finds out.
Roger Ebert panned The Dying Gaul basically for having no redeeming character, but each character has their own highs (which are relatively middling) and lows (which get shockingly low). This was also Ebert's problem with MouseHunt. Essentially, the movie never really decides whose side we're supposed to be on. You can't fault the brothers, who are flat broke with sympathetic backstories, for wanting to get back on their feet. Nor can you blame the mouse for defending its home and its life. At the film's close however, it manages to subvert this by giving both sides a Happily Ever After. This trope is also true of the majority of the Tom and Jerry shorts which this movie borrows heavily from, so perhaps it was done on purpose.
Rush goes out of its way to not pit either James Hunt or Niki Lauda as the 'hero' or the 'villain' in the story. Neither are bad people per se, just two very different people with two different and equally valid lifestyles and driving styles.
As Will points out in Transcendence, RIFT wants to take down potentially useful technology, and they won't hesitate to kill anyone to do so. On the other side, Will's move toward hybridization and group consciousness, no matter how peacefully he goes about it, is seen as a threat by everyone, including his closest friends and his wife.
The fraternity from Neighbors, especially Teddy, are depicted surprisingly sympathetically, while Mac and Kelly do some pretty dark things during the feud. Neither side comes across as fully bad or fully good.
In Thank You For Smoking, the Merchants of Death, for the most part, are pretty unscrupulous, but while the actions of the MO+D Squad are questionable, they don't cross any serious lines. But their opposition, Senator Finistirre isn't above a bit of manipulation, either.
In Dawn of the Planet of the Apes, there's really barely a single wholly unsympathetic character in the entire film. Out of the film's main antagonists, Dreyfus is more misguided and ill-informed than malicious and Koba has a solid Freudian Excuse for hating the humans and fearing what they could do if given too much lenience. Even Carver, the Jerkass who accidentally kicks off the hostilities with his bad behaviour, is clearly acting more out of fear and misplaced blame towards the apes than malice or sadism. Rise as well. Yes, the apes have good reason for rebelling, Humans Being Bastards of course, but it's not like the experiments being conducted on them were for the fun of it.
Vera Drake. The film revolves around a back-alley abortionist who is keeping her profession a secret from her family. No one on either side of the issue, with the arguable exception of her son Sid, is portrayed as heroic or villainous.
In Chung Kuo, there is no really good side; both the Han rulers and the European rebels commit atrocities as the story progresses
The War between Manticore and Haven in Honor Harrington, with the second Haven revolution in the series resulting in a government led by good people, has become this. Indeed, as this carries on it's lost even much of that, becoming more of a Let's You and Him Fight between good guys.
As of Mission of Honor, the governments of Manticore and Haven realize they were manipulated into their wars, and ally to fight Mesa, which is responsible for their troubles.
Featured very prominently from the second series onward in Warrior Cats. The authors have even gone back to write sympathetic backstories for most of the villains, the most notable being Scourge. Tigerstar and Hawkfrost are also noteworthy because, although they wanted power and did horrible things to get it, they only wanted power because they believed they could do a better job of running the Clans and help keep the forest peaceful (Although Tigerstar's vision for running the Clans was very racist). The villains of the fourth series also consist almost entirely of cats that have been wronged or forgotten and are rising up for revenge. Then for the heroes, we have Brambleclaw, who had the exact same goals as Hawkfrost, and leaned dangerously close to The Dark Side, making Hawkfrost's status as a Manipulative Bastard pretty much the only difference between them. We also have Leafpool and Squirrelflight with their (spoileriffic) lies and betrayal. And then there is Hollyleaf, Lionblaze and Jayfeather, who all seem to be much more dysfunctional than all the other characters.
And then there's Sunrise. You could argue all you want over who was most responsible for the angst-filled mess that is the ending, but the most reasonable explanation (and the one that causes the least headaches) is that everyone was in the wrong to a certain degree.
And Tigana covers the whole spectrum. You've got the sympathetic and "good" Devin and Dianora, then Alessan, Brandin, and Alberico. In other words, it's more like White and Gray and Darker Gray and Black morality.
Animorphs falls under this tropes in the later books. At first it's a pretty clear cut case of the bad guys (the Yeerks, taking over the planet parasitically) and the good guys (the Animorphs, and by extension the Andalites, who also hate the Yeerks). As time wears on, however, it's revealed that the Andalites response to the Yeerks infesting the Hork-Bajir homeworld was to release a deadly virus into the atmosphere of the planet, killing nearly all Hork-Bajir on their homeworld. If the Animorphs fail to stop the Yeerk invasion, the Andalites have plans to do exactly the same thing to Earth. As well as that, some of the Yeerks start to be portrayed as true characters, with individual motivations and emotions, instead of just a pack of slugs. Even the Taxxons, giant centipede-like creatures get some of this; they're revealed to be total slaves to their own hunger, literally unable to stop eating as long as there is food around. Then there are the Animorphs themselves; over the course of the books they morph from idealistic kids doing the best they can to a hardened guerilla force with no qualms about sacrificing the new bunch of idealistic kids in the name of winning the war. This seems to have been the point of the series.
The Kommandant's Mistress. The entire book is based on a concentration camp Kommandent and a Jewish inmate, who respectively are not entirely a villain and not entirely a victim.
The Chaos Walking trilogy is all about this. While Mayor Prentiss is a darker shade of gray, Mistress Coyle and the Answer's methods of stopping him (no matter what the cost) can be those of a terrorist or a freedom fighter. This is heightened when the heroes are forced upon the two different sides, while being aware of how much rubbish the whole war is. Also the fact that it's practically a gender battle heightens the uncertainty of the war. In the third book they team up in an alliance against the Spackle, even though the Spackle are the ones that were treated so terribly
The Reynard Cycle draws the very clear distinction that behaving heroically doesn't always directly translate to behaving ethically or morally. It also portrays the majority of its villains as driven by understandable (occasionally even laudable) goals and motivations. That said, several Complete Monsters tend to keep things fresh.
The Star WarsExpanded Universe flies up and down the morality scale Depending on the Writer; most of them have pretty clear bad guys, and with Timothy Zahn most of those bad guys aren't so bad, but his book Outbound Flight fits here. There are a lot of major characters, but they end up falling into one of three categories: Jedi and civilians on Outbound Flight, Chiss and captives, and Darth Sidious's agent. None of those are entirely good or evil. Outbound Flight is led by Jorus C'baoth, an arrogant and domineering Master who believes himself to be the ultimate authority, and whom the others are reluctant to contradict. The main Chiss character is Thrawn, who... well, he's at his most heroic here, but he'sThrawn. Sidious's agent is planning to destroy Outbound Flight, but he doesn't exactly cackle and he respects Thrawn. The few unambiguously Good characters have subplots, but in the end all they're able to do is die to save fifty-seven out of the fifty thousand who were on Outbound Flight.
On the one hand DORLA in Kit Whitfield's Benighted uses police state tactics and functionally, if not officially, operates on a "guilty until proven innocent" mentality. On the other hand they do a dirty, dangerous and very necessary job and get less than zero appreciation for it from the public.
There's an interesting variation on this trope in Jack Campbell's Lost Fleet series: the protagonist wakes up from almost a century in suspended animation, having been "killed" in the first battle of a presumably White on Grey war, to find the same war still raging, but with both sides reduced to the lowest possible moral levels as a result of ridiculously high attrition and a circle of atrocity and counter-atrocity. Being understandably appalled at this, he goes on to teach his fleet about honour and efficiency to move it away from Black on Black to Black and Gray Morality before exploring the mindset of his Syndic enemies (upgrading them from Black to merely ridiculously inefficient dark Grey). And then it turns out that there are ineffable aliens (with their own morality altogether) behind it all. By the end of the story, Geary only manages to deal with the aliens by completely defeating the Syndics first and getting to the other side of their territory.
In the A Song of Ice and Fire series and its television adaptation, no one major faction is wholly good or evil — each has its own unique positive and negative traits; it's the methods they choose to use that decides whether they are face or heel:
The Starks are "heroic" because they are honorable to a fault and prefer diplomacy over warfare. Despite this, one of their most useful bannermen is Roose Bolton, who is tolerated as a Token Evil Teammateuntil he finally does betray them, and testimony from peasants in the wrong place at the wrong time show that Stark grunts do Rape, Pillage, and Burn just as much as the Lannisters.
The main Baratheon family is a mixed bag, because King Robert is shown as a charismatic ruler who is at least Genre Savvy enough to surround himself with able advisers. On the other hand, his son (by his wife Cersei through Brother-Sister Incest with Jaime) Joffrey is psychotic, immature and capricious, with his only redeeming trait being his yearning to win his father's approval.
Renly Baratheon's faction is "heroic" because they fight honorably and have several noble warriors on their side, but are fools who still are fighting a bloody war for personal honor and power.
Stannis Baratheon's faction is "villainous" because they use incredibly creepy Black Magic and assassinations to accomplish their goal which is ultimately noble. This is finally proved when Stannis, at Davos' insistence, finally realizes that if he is a true king it is his duty to protect his subjects by temporarily putting his ambition on hold and going to the Wall. So far, he is the only ruler to actually accept responsibility in this way.
Daenerys Targaryen is "heroic" because she is fighting to reclaim the Iron Throne, despite being constantly reminded that her father, Aerys II, was a lunatic, and that commoners would rather be left alone. She initially believed that the commoners secretly prayed for her return, but even when disabused of this notion she still thinks of wreaking revenge on the "usurpers" instead of considering if Westeros even wants the Targaryens back in the first place. As the story progress she becomes a crusader against slavery and exploitation but conquers whole cities in the effort to eradicate the practice which proves equally problematic. She also shows no remorse for ordering deaths, including burning a woman alive.
Varys is "villainous" because he is one of the top chessmasters of the brutal civil war, who did as much as anyone to bring it about, but his claim that he genuinely cares for the realm makes him more sympathetic to some readers, especially as compared to his intellectual rival, Petyr "Littlefinger" Baelish, who is an outright sociopath. On the other hand, certain of his actions make it clear he's only interested in stability on his own terms, as seen when he kills Kevan Lannister just when he was starting to pull King's Landing back together after Cersei's reckless craziness.
Kevin J. Anderson's Terra Incognita series. Examples ranging the spectrum from the very good to the very evil can be found among both the Aidenists and the Urecari while the Saedrans stay strictly neutral.
The Old Man's War series: The Colonial Union really wants to protect and preserve the human race in a universe full of hostile aliens who want to eat them. But they're basically a military junta using some questionable, authoritarian methods: recruiting the majority of their soldiers from a planet (Earth) kept completely in the dark about the rest of the universe, and vat-growing a group of emotionally-stunted, effectively Child Soldiersfrom the bodies of the dead as Special Forces, restricting civilians from certain technological advances, and engaging in aggressively expansionist wars of colonization, steadily turning the rest of the galaxy against them. On the other side, there actually are many hostile alien races who want to eat humanity, but most end up joining the Conclave out of a desire to use diplomacy to try and minimize aggressive war and further bloodshed.
The three empires in the Quintara Marathon series demonstrate this, at least in terms of the humans who are represented in all three. The Exchange is a free-market free-for-all with the most personal freedom, but minimal social safety nets and an underbelly of corruption and unofficial slavery (in the form of genetically engineered intelligent beings considered as property). The Mizlaplan control a rigid theocracy where they are unquestionably the rulers (and effective gods), inquisitors and priest can use whatever methods they feel are necessary, sexual discrimination against women is part of the system, and where brainwashing into absolute obedience is commonly used, but where most people live peaceful, safe lives without concern about going hungry, crime, or actually being personally oppressed. The Mychol Empire is a dog-eat-dog vicious society with oppression, slavery, and a great deal of violence, but where everyone has the opportunity to rise if they are smart enough.
In Lonely Werewolf Girl no one is really heroic; Kalix killed her father, Sarapen is batshit insane, the rest of the werewolves downright callous and manipulative, Moonglow cheats on her boyfriend, Daniel is trying to be a Dogged Nice Guy to Moonglow, Malveria a Retired Monster, and the Avenaris Guild of werewolf hunters are trigger happy sociopaths.
The Civil War in Bernard Cornwell's Starbuck Chronicles. This is because rather than deal with the causes of the war he approaches it from the perspective of the individuals on both sides and finds that there are heroes and scoundrels on both sides. Emphasized by making the viewpoint character, Nathaniel Starbuck, a "Copperhead" (a Northerner who sided with the South) and another major character, Adam Falconer, a "Scalawag" (a Southerner who sided with the North).
Gone, by Michael Grant. All the characters are kids under the age of 15 who are trapped in a bubble without adults. On their 15th birthdays, they disappear, too. That's called the "Poof". The heroes are trying to figure things out, put things back to normal, learn how to use their new powers, and figure out how to survive their 15th birthdays. The villains have mostly the same motivations, except that their methods are different. The heroes sometimes do bad things, and the villains sometimes do good things. Basically, they all just want to survive. The exception is Drake, who Michael Grant has confirmed is pure evil, no shades of gray. Penny is also wholly evil.
Fugue for a Darkening Island invokes this trope, 70's Britain split into civil war as thousands of African refugees flee into Europe to escape a nuclear war. The refugees are innocent and desperate, but often violent and thuggish. The fascist government is cruel and oppressive, but the only thing preventing the total collapse of the country. The secessionist movement is liberal and free, but weak and elitist.'
Paolo Bacigalupi's The Windup Girl is very dark grey on all sides. The calorie men are out to make profits by whatever means necessary, but they're also trying to stave off unending waves of plagues and blights. The Kingdom of Thailand heroically resists the outsiders who want to plunder it, but it's also deeply corrupt and politically unstable. Hock Seng, who appears ready to do anything to save himself, also has one of the most depressing backstories, and when we last see him, he is risking his own life to save a little girl. A character who looks heroic will turn out to have something very dark in their past (or present), while one who looks villainous may have honorable intentions.
David Drake's Hammer's Slammers does a good job of showing how this trope appliesinwar; both the titular mercenaries and their opponents do some prettydespicable things in order to hold their own losses down, like nuking a rebel stronghold because attacking it any other way would result in unacceptable losses for the attackers. When the series deviates from Gray and Gray, it's usually to go to Black and Gray, especially if MajorJoachim Steuben is involved.
Keys to the Kingdom has a lot of this as well. Dame Primus is quite The Chessmaster, and not in a good way. The only truly good character is Arthur, and he barely has any idea what's going on for a lot of the time.
In The Kingdoms of Evil: The main character is put in charge of all the evil in the world. Next up, figure out what the hell evil actually is.
Jodi Picoult's My Sister's Keeper. On the one hand, we have a mother who is desperate to save her daughter's life, even if it means subjecting her other daughter to a variety of increasingly invasive medical procedures against her will. On the other hand, we have a girl who doesn't want to undergo dangerous and painful medical procedures anymore and wants to be seen for herself rather than as replacement body parts for her sister, even if it means taking away her sick sister's last chance at survival. Welcome to the world of no right answers, folks.
Summarised perfectly in this quote from Anna:
Anna: Even if we win, we don't.
Jodi Picoult, period. "No right answers" is pretty much her stock in trade...
The first book of the Artemis Fowl series has this in spades. Artemis freely admits that he's a greedy, manipulative villain, but he aims to use the gold from his kidnapping/extortion scheme to find his lost father and his mother is millimeters away from a nervous breakdown. The LEP just want their officer back without paying any gold, but they go through some very dark means to get it and even intend to kill Artemis if none of their other plans succeed.
The soldiers and rebels in Beachwalker are both portrayed as having sympathetic members, and the book entirely avoids taking sides in their conflict, focusing instead on the specific combatants and civilians in the protagonist's immediate sphere of influence.
Black Company by Glen Cook at best. Most prevalent in the first book, and then appearing here and there throughout the series.
The people on either side of the diamond wall in Dirge for Prester John view themselves as the real Pentexore. Neither side is more valid than the other, just one side has the benefit of the Fountain of Youth.
All sides in The First Law trilogy have a mix of good, evil, and indifferent. Then groups of good guys from a mostly evil faction will have a Token Evil Teammate. Then that evil guy might have a good side. It is a mess where an avowedly morally indifferent protagonist character from a corrupt faction of the nominal good guys recognizes that someone's treason was probably the morally correct decision while still pursuing his country's aims. Another book follows a war with protagonist characters on both sides.
In Michael Moorcock's book; The Eternal Champion, the humans are seen as good for the first approximate fifth of the book, but as the story progresses the humans are switched to being about on par with the Eldren (Humanity's inhuman enemies), and towards the end, even Ambiguously Evil.
Black Crown: Depending on your views about the conflict in 'Schism', either side could easily be seen as a reasonable way to deal with the situation. May become A Lighter Shade of Grey for whichever side you take.
In The Dresden Files, aside from Harry and his friends, a large number of groups aren't quite so cut and dried.:
The White Council, portrayed as axe-crazy templars in the first few books (due to picking on Harry personally), are later shown to not only genuinely be serving their greater good, but that that good is actually the best of a lot of bad options.
The fae courts are more Blue and Orange Morality than black and white to begin with, but the almost-human members and even many fae seem to have the same mix of malice and innocence as vanilla mortals.
Gentleman Johnny Marcone is a gangster of the Al Capone school, and thinks nothing of murder to protect his business interests... but he hates inefficiency with a passion and prevents more "unnecessary" murder than the entire police force put together, as well as suppressing rivals' crime on his turf. There have been hints that the police aren't so much afraid to go after him as that they simply don't want to, as his way is preferable to disorganized crime.
Harry himself has slipped off of the slippery slope more than enough times to qualify as more gray than white, though in his case it's at least not typically willingly— something that the people on his side regularly assure him still puts him firmly on the side of right, and everyone else isn't so sure of.
This is a major element of The Truth About Celia Frost. Dr. Hudson even lampshades this:
Celia: I understand the difference between right and wrong, and what you've done is wrong!
Dr. Hudson: You're being naďve. Wouldn't it be simple if everything was really as you see it? Black and white, right and wrong. But I'm afraid life is more complicated than that. Those messy grey areas keep getting in the way.
The Mirrorworld Series: Kami'en and the Goyl versus Empress Therese and the Imperials. The Goyl seem like the logical villains until you find out more about Therese's ruthless tactics. Not to mention, their hatred of humans is a natural response to years of human aggression. Then again, Therese and Austrya aren't entirely unsympathetic either...
The Nexus Series: Multiple factions come into conflict over how to use the titular Nexus 5, which allows a user to have a permanent and unobtrusive Brain/Computer Interface. The developers of said technology just want to see how many cool things they can do with it, believing the benefits outweigh the risks. As soon as the technology becomes available however, terrorists and criminals begin using it to create slaves and suicide bombers. At the same time, parents of autistics use Nexus to communicate with their afflicted children and help them socialize. People using Nexus start to resent being subjugated by the anti-transhuman laws designed to protect the rest of the populace, and some are driven to become exactly the monsters that the laws were drafted to fight. With very few exeptions, it's pretty hard to write one side or the other off as being completely in the wrong.
Kindling Ashes: Each side believes that this is a case of Black and White Morality but the dual protagonist system shows that each side has grievances. One dragon recalls how humans killed his mate, broke his Flyer, and smashed eggs, while in the next chapter, that human recalls how that same dragon teared down towers and burned humans alive.
In Czech fantasy/horror series Hammer On Wizard (roughly translated as Kladivo Na Čaroděje) is second to none line between good and evil. Almost everyone there is motivated either by money, career, saving his/her sorry butt or some personal reasons better left unknown. Living in Crapsack World, where No Good Deed Goes Unpunished plays a role too.
In ''Dark Ones Mistress" the MC Clarabelle learns the ruler of her kingdom (the Dark One of the title) uses criminals in the royal army, keeping them leashed by way of stealing their souls. Innocents people sometimes get caught in this web and while killing him off is the only way to free them, it would basically unleash hell on the populous.
Daniel Abraham's The Dragon's Path, book one of The Dagger and the Coin series, has, as one of its most sympathetic, likable, and humane characters, a mass murderer who burned down an entire city, killing thousands of innocent civilians, out of pride. One of the main conflicts is between two factions of aristocrats, one of which wants to liberalize the empire, allowing greater representation within government to the common people, but which is willing to use assassination and treason to accomplish its ends, and the other, which is trying to maintain the privileges and powers of the aristocracy, but is more honorable and patriotic.
Bear in mind, however, that subsequent books in the series become less grey, as the guy who burned down the city in book one becomes a lot less sympathetic. He has Jumped Off The Slippery Slope by book three at the latest, and may even have passed the Moral Event Horizon by book four.
All My Children: Regardless of being designated heroes and/or villains, very few characters in the series could truly be considered clear-cut good or evil, especially if they have criminal pasts. Erica and Kendall alone have both committed enough crimes, both individually and equally, to pile-drive them into federal prison for a very long time.
Torchwood has numerous examples of good guys (Jack in particular) being less than good, and 'bad' guys just acting within their nature. Witness the Children of Earth miniseries; the faceless, completely evil aliens are the plot's driving force, but the meat of the story is what the government and what Torchwood are willing to do to deal with it. It's hard to say if anyone wins in the end...
It was common in the show's early historical episodes. The Crusade shows both Richard the Lionheart and Saladdin to be honourable men.
Doctor Who and the Silurians is a textbook example as both the humans and the Silurians are shown to be equally aggressive and honourable, with even the Brigadier commiting attrocities to win.
The Caves of Androzani depicts a brutal war between the military forces run by a well meaning but ruthless General whose willing to execute civilians when ordered even if he believes they're innocent, and Jerkass Woobie Sharaz Jek, a lechy drug runner whose been driven mad by the treachery of his former partner Morgus and helps the Doctor in the end.
The Vorlons and the Shadows in Babylon 5 — eventually. The conflict is definitely black-and-white for the first three seasons, but then swerves into grey-and-gray shortly before the war ends.
JMS pointed out in first season commentary that he was proud to have pulled this off when the Vorlons were just as prone to blow stuff up with no real justification.
JMS also stated that the actors who played Londo and G'Kar were asked to flip a coin to see who would be the "good" one. He was immediately asked: "Who won?"
The joke makes a lot of sense in hindsight given that Londo and the Centauri are initially portrayed almost wholly sympathetically, while G'kar and the Narn are portrayed very much as villainous. By the end of the second season, however, both the characters' and audience's sympathies have completely reversed (in part thanks to Londo making a Deal with the Devil). By the end of the fourth season, it's no longer clear who's the hero or the villain in the perpetual conflict - which was almost certainly the intention of Stracyzinski from the very beginning.
By The Sword Divided. There are some obviously 'good' characters, but none of them are perfect, while no one is shown as an out-and-out villain either.
The new Battlestar Galactica started off with the Cylons nuking the entire twelve colonies (ostensibly in retribution for the human's mistreatment of them before the first Cylon War) and the surviving Colonials running and trying to find Earth in a rag-tag fleet. However, as the seasons went on, the Colonials were shown more and more as people who could compromise their morality to survive, ultimately culminating in the arrival of the Pegasus and Admiral Cain, who not only allowed torture, but allowed her sole Cylon prisoner to be raped over and over again. Near the end of the second season, the episode "Downloaded" also showed a different side to the Cylons ? some even thought the destruction of humanity had been a bad thing. This eventually resulted in an Enemy Civil War and the end of the fourth season saw an alliance between the Colonial Fleet and the Rebel Cylons.
In various seasons of Survivor, the final two (three in more recent seasons) was often seen as this, both (or all three) people pretty much annoyed the Jury and they wound up voting for who they viewed as the lesser evil.
Marquesas is perhaps one of the best examples of this trope; Neleh admittedly didn't start playing the game until Day 24 and glided through on other peoples' shoulders, while Vecepia flip-flopped enough times to make everyone question where she stood, and won because everyone was mad at Neleh.
Thailand - Brian was a cold emotional sociopath who barely even spoke to the other tribe, and was accused of sexism and backstabbing among all things, while Clay was accused of racism and generally being a lech. Brian won only because he had enough people who respected him on the jury.
All-Stars: Rob and Amber were both blasted by the jury with Rob being viewed as a manipulative snake and Amber as a coattail rider. Amber ultimately won by one vote because of how mad the jury was at Rob.
Samoa is another example. Most of the jury was indeed angry at all three, who either rode coattails to the end without contributing much on their own and saying they deserved it in real life, (Mick), rode coattails and played dumb (Natalie), or wantonly bullied their way through the game and bragged about how awesome they were (Russell). Ultimately the vote was overwhelmingly towards Natalie - not for her strategic play or physical prowess, but because the jury thought she was a legitimately nice person.
South Pacific - Albert was seen as a sleaze and someone who nobody liked or respected, Sophie was seen as a pretentious and condescending brat, and Coach was accused of using religious hypocrisy and breaking his word several times over despite claiming to play with "honour" and "integrity". Ozzy laid it out in his opening jury speech - the jury did not want to vote for any of them.
In LOST the issues are so complex and the characters so murky that no one seems to be pure good or evil, although there are definite shades of gray (Hurley for instance is pretty light while hell, even Ben is getting truly gray.)
Dollhouse. While what the Dollhouse and the Rossum Corporation do is clearly nightmarish, and Paul Ballard (and earlier, Caroline) must be right to want to bring them down, Ballard is prepared to do very dubious things to do it, while Caroline is irresponsible and quixotic. Meanwhile, the people who work for the Dollhouse seem to really believe that they're doing good by "giving people what they need", and the dolls are all volunteers...
DeWitt's house, at least, seems to recruit people in desperate straits and helps them establish new lives after their term is finished. Whether this is rescuing them or preying on those with no options is an exercise for the viewer.
The episode where we first see Tudyk's character, Alpha, really shows the G&G. The start of the episode shows Echo saving a young girl from a downward spiral and helping her get over her traumatic past, while Ballard sneaks into the Dollhouse after finding it, accidentally bringing Alpha with him and causing problems while trying to help.
For added gray bordering on Fridge Horror, consider Boyd's stated reason for harvesting Echo's spinal fluid. If the antidote he could have synthesized was used properly it could potentially have saved thousands of people from being wiped, imprinted, bodystolen, and killed and may have severely mitigated the eventual downfall of civilization depicted in the season ending episodes.
In Merlin, the boy wizard himself and Arthur are definitely good guys. But they support a Knight Templar king who would execute Merlin if he knew the truth, often against designated villains with a legitimate grievance, and Merlin often makes some questionable choices to balance his nature against his support of the king. Why? In Arthur's case, family loyalty; in Merlin's it's just Because Destiny Says So ("destiny" in this case being a dragon with a fairly major grudge against Uther himself). Hence, when Morgana decides to side with Morguase, it's very hard to see it as a Face-Heel Turn, and the script doesn't really make much attempt to present it as such.
The Wire is one of the finest examples of this trope in any medium. While you may arguably root for the cops to make their case, it's impossible to see even most of the cops as good guys. And the criminals get far too many humanising moments to possibly be considered bad guys. Creator David Simon said he wasn't interested in doing good vs. evil anymore; the results were as far in the opposite direction as can be done. While the politics remain consistently gray, as do the inner workings of the police department, in the conflict on drug kingpins, whenever Marlo Stanfield and his crew are involved, the show arguably crosses over into Black and Gray Morality.
Dexter, especially when it comes down to Dexter vs. Doakes in season 2. In the words of the man himself:
"Am I evil? Am I good? I'm done asking those questions, I don't have the answers. Does anyone?"
He also points out that he essentially does Doakes' job but "at no cost to the taxpayer", and says that Doakes only knew he was a killer because he was one himself.
In stark contrast to other Trek series, Star Trek: Deep Space Nine is pretty much built on this trope, with the protagonists being A Lighter Shade of Grey. Hell, just watch "In the Pale Moonlight"... or listen to Kira talk about her days in the Resistance.
In a fifth-season episode, "The Darkness and the Light", someone is targeting members of Kira's former resistance cell. She finally identifies the killer a Cardassian servant disfigured in one of their bombings. He claims, persuasively, that she killed innocent people whereas he never did-such as a bomb she set taking out not only a brutal Cardassian war criminal but his entire family too, along with anyone in the immediate vicinity-whereas he goes out of his way only to target them, and even spare the life of the unborn child she's carrying. Kira retorts that every Cardassian on Bajor during the Occupation, even if they just ironed shirts instead of carried a weapon, was equally guilty and were all legitimate targets. True, she's talking with a calculating, cold-blooded killer, but it drives home that, yes, Kira was a terrorist, and from his point of view he is the "light" to her "darkness". Kira's only real reply is the old idea that the one cannot exist without the other, or as she says "the light is brightest in the dark."
During its first three series, The 4400 featured several distinct factions (NTAC, the 4400 Centre, the people from the future, the Nova Group, Jordan Collier and his followers, Dennis Ryland's company), all of which are shown as in some way sympathetic, with good intentions. It's not until series four that we finally see some unambiguously bad guys (The Marked, who want to stop the 4400 and bring about the apocalypse just to make sure they stay on top of the pile).
While Fringe often presents wholly evil villains of the week, the war between parallel universes has oodles of this trope. The person most directly responsible for starting the conflict is Walter, our loveable Mad Scientist good guy, who kidnapped his Alternate Universe counterpart's child: the subsequent actions of Walter, William Bell, Walternate and both Fringe Divisions are attempts to defend their home universes from the other side's "attacks". Neither universe is depicted as "evil" or malicious. Walternate's ruthless, but he's faced with a world that's collapsing due to Walter's actions and believes it's the result of a deliberate attack by "our" universe. Also, Walter conducted experiments on children, a line Walternate was unwilling to cross.
La Femme Nikita — the 1997 Canadian series, not the reboot — may not be a great show, but it did a superb job of gray vs. grey, so good that it's worth watching just for this. Everyone is compromised, no one has clean hands, the intertwined layers of greater and lesser evil get extraordinarily complex, and the hero (or anti-hero) manages to embody the trope to near perfection—despite some truly cringeworthy writing and character assassination. Even the luminous, golden-haired heroine fits the trope by the middle of the first season. Signaled conveniently by the all-black dress code for most characters.
Covert Affairs: While there are some definite bad guys, a lot of their enemies are decent people that simply happen to be working for their particular country just like Annie and her friends in the CIA are working for their particular country.
As The Borgias takes place during the power struggles between the rival Italian states and factions of the Renaissance, it fully embraces the moral ambiguity of the period, with few genuine heroes or outright villains. The Borgias don't shy away from using deplorable means to secure their power while continuing to do sympathetic things. Their enemies are not much different, and are defined as villains more for opposing the protagonists of the series than much exceptional vileness compared to the Borgias.
On Salem, the conflict is of dark witches versus brutal witch-hunters. This could even be Evil Versus Evil, with innocent people such as Bridget Bishop and Giles Corey caught between the "grand rite" of the witches and the zealousness of the witch hunters.
John lampshades this in his last conversation with Cotton.
The Christmas special in the Norwegian sitcom Mot i Brřstet has Karl set up as the bad guy because he insists that they should celebrate Christmas in the old fashioned way, much to the other's displeasure, but the rest are wishing expensive gifts from him since he earned a lot of money on the stock market.
French singer Jean-Jacques Goldman titled one of his songs "Entre gris clair et gris foncé" ("Between Light Gray and Dark Gray"). Specifically, its lyrics are about the increase of ambiguous morality in fiction.
The Norse view of the world was pretty much entirely founded on this trope. While the Gods weren't all that bad, Odin could be an unreliable jerkass and tended to decide men's fates on a whim. Similarly, despite their horrific nature, the Gods' enemies could be portrayed as sympathetic, especially in the case of Loki. He constantly broke rules, but on the logic that too much order would stifle creativity. The real conflict is more one of order versus chaos, although it's clear which side the audience was rooting for.
Reynard the Fox fables evoke this. Reynard is a trickster, and frequently the bane of other characters, but all characters are flawed. They are all animals (just like we are) and act according to their instincts. Reynard is the folk hero, but is not "good" or "bad", he is just as flawed as all the other characters.
Similarly, Wolf and/or Coyote, depending on the region and tribe (and even storyteller). Sometimes, he's a Prometheus-like creature who stole fire from the Gods to give birth or help humanity. Sometimes he's just looking for a meal, and isn't any more harmful than Bugs Bunny. Sometimes, he's a rapist coward who murders men, women, and children by tricking them into deadly games. One rape of a woman lead him into pitying her and helping her give birth, while others have him return food and protect those he stole from. He's a complicated case.
Rose: Those of us who fight for good, even as grey as we are, do our best to save as many lives as we can. We do the best we can, but sometimes we have to make sacrifices. Sometimes we do unsavory actions like lying, cheating and stealing. Like taking bribes, helping criminals, or killing unsavory people. But despite all our problems we are still trying to do the right thing.
While individual conflicts often have more clearly defined heroes and villains, almost every major faction in the BattleTech universe is ultimately like this, and many characters are simply soldiers and commanders doing their job for their respective cause.
The only faction that could truly be considered evil was the Word of Blake, and they didn't become true villains until 20 years after the setting premiered.
Exalted. While the various demons, undead, and The Fair Folk are usually portrayed as antagonistic (and even then, there are exceptions), the various human and Exalted factions all have plenty of good people mixed in with the villains, selfish bastards, and crazies.
The only being that, no matter what point of view, is in fact, in the black side of the scale, no matter how you look at him, is the Ebon Dragon, who is pretty much the literal embodiment of dickery, evil, and opposite to all virtues. He created the Unconquered Sun, so he could have something to be the opposite of. He also invented betrayal.
Even then, he's still somewhat sympathetic in a pathetic way. He literally can't be anything but The Supreme Dick in all of existence. This of course raises the question of whether anything in this setting (Or even Real Life) can be said to be pure evil if you can't choose to be it, but that raises philosophical questions beyond the scope of this Wiki, so let's just leave it at that.
Planescape. Factions aren't explicitly good or evil, they just have different motivations and can commit a variety of acts.
In the Dungeons & DragonsWrath of the Immortals campaign, the two principal factions of Immortals (D&D's functional equivalent of AD&D's gods), the Ring of Fire and the Fellowship of the Star, both have good reasons for what they do, and both pursue their objectives by morally questionable means. Rad and his followers in the Fellowship of the Star are just pursuing knowledge, and are studying a magical artifact, the Nucleus of the Spheres, that has incredible powers that are unique in the universe, and might possibly be used to make the world a much better place. The problem is that the Nucleus is draining the magical energy from the world, which would, among other things, exterminate every magical race, including elves, dragons, fairies, etc., meaning several counts of genocide. To say nothing of all the other people who would die as the civilizations, most notably Alphatia, that depend on magic would collapse. So Ixion and his followers in the Ring of Fire have sound reasons to want to destroy Rad and stop anyone from using the Nucleus of the Spheres. As things develop, however, the only way to destroy Rad is to kill all his mortal followers, meaning that Ixion and his allies have to provoke a war by Alphatia against Glantri, a war which drags in Thyatis and the Heldann Freeholds as well, and which ultimately spreads to many other countries, killing millions. But neither is side really wrong. The Brotherhood of Shadow, a third group of Entropic Immortals who are just trying to prolong and exacerbate the conflict are straightforwardly evil, except that their scheming is both pretty ineffective and, even more importantly, enables the heroes to figure out the whole plot and save the world. So the good Immortals unleash a war that kills millions of innocent people, while the evil Immortals are relatively ineffective at making things worse and inadvertently save the world. Go figure.
Into the Woods uses this in relation to fairy tales; for example, Jack might be the hero, but he still killed someone's son. The point of the musical is to show that people are not good or evil, but just people.
The main characters' dilemma in the second act is choosing whether they want to give Jack to the giant and save themselves or spare him and let the giant kill everyone in the kingdom.
Peer Gynt plays this straight on the title character. Come the fourth act, he lampshades it heavily, relating this as his philosophy of life: balancing out the bad deeds with good ones. For instance, he deals with slaves, and also trades in pagan idols. For every pagan idol he sells, he makes sure a heathen is baptized.
Brink: The developers said they wanted to avert both La Résistance vs The Empire, and good cops versus evil terrorists. And did they do it well! To illustrate, their respective leaders, Chen and Mokoena, are both decent and morally dubious alike in their own way. They both have noble goals: Chen wants to send a scouting party to find land and have equal resources and rights for Guests and Founders, and Mokoena doesn't want the Ark to descend into anarchy and wants them all to work together, and is just trying to keep the ark safe. And its also made clear that the Resistance and Security have their fair share of the "I'm doing what I have to" and "total bastard" mentalities.
EVE Online has thiss—every major (and all the minor ones too) have this in droves. The capsuleers, on the other hand, have Blue and Orange Morality as a result of being immortal spaceship pilots neurally connected into their very ships and being subjected to an unending cycle of being killed and resurrected in a clone.
The Gallente Federation are all about [[Eagleland freedom, democracy, and self determination]]. Except when they brutally crack down on dissent in the wake of the Empyrean Wars, turning into a brutal police state. Also, their conflict with the Caldari really only started when they forced them off their homeworld for wanting out.
Also, they're French.
The Caldari State is a ruthless, hypercapitalistic society run by Corrupt Corporate Executives where you are a citizen of your megacorporation, not the state itself. They also have this nasty militaristic tendency. However, all their militarism is motivated by their desire to reclaim their homeworld from the Gallente and they are the one true meritocracy with actual social mobility in New Eden.
The Amarr Empire bring order, civilization, and progress to a desolate galaxy. They also bring enslavement, indoctrination, and religious zealotry in their fanatical belief that conquering New Eden is their destiny.
The Minmatar Republic are former slaves who overthrew the chains of repression and are fighting to free their brothers and sisters still trapped under Amarrian tyranny. Which would be great, if it weren't for the fact that they are a fractious, bickering group of tribal peoples with a standard of living along the lines of a third world country.
The Angel Cartel appear to be this, too. They are competent (more so than the Republic) and they are quite popular whereever they rule. A storyline event even involved a group of Minmatar systems voting to be moved to under the control of the Cartel. However, they are still a criminal organization with their fair share of dirty laundry, engaging in slavery, drug-trading, kidnapping, and terorism in general.
S.T.A.L.K.E.R.: The conflict between Freedom and Duty is this, combined with Order Versus Chaos. Duty are a faction of grizzled ex-military types who believe The Zone is an abomination that threatens the world and should be destroyed. Freedom are a group of anarchists and thrill-seekers that believe The Zone is a miracle that provides beneficial eldritch artifacts and therefore should be freely accessed by the public. Neither is especially nicer than the other, and they both have their share of dicks and nice guys.
This is a major theme in Pokémon Black and White, which pits the protagonist, Unova Gym Leaders, and other characters (united by their love of battling) against the Animal Wrongs-leaning Team Plasma. Each side decries the other's morality as misguided and hypocritical, and many fans found themselves siding with Team Plasma - or at least against the "good guys."
The Succession Crisis in Dragon Age: Origins. The Dwarf origin stories give you some pretty clear reasons for supporting each. Commoners would want to support Bhelen because he fights to end the oppressive caste system and wants to open the country more to the outside. Nobles would want to support Harrowmont because it's their father's wishes and he's more "Traditional". You also have a personal reason for doing so, Harrowmont is a very nice guy and a Reasonable Authority Figure, as he fights hard to make sure the dwarf noble is given a fair trial. Bhelen meanwhile fights hard to get to the throne...to near sociopathic levels, as he's rightfully suspected of killing his older brother and getting his other sibling blamed for it. note The noble even has a chance to call him out on this, during which he has almost no remorse for it unless you compliment him and say he was better at playing the game Oh, and to keep things up, Bhelen, if chosen, becomes a dictator who leads his city into a new era of prosperity. Harrowmont meanwhile dies partly due to the stress of ruling and causes Orzammar to fall into decay while expanding its isolationist practices.
Just about all of Dragon Age II which manages to be even grayer than its predecessor. The mages, chantry, and qunari are ready to tear each other apart and all of them have good people and bad people or have different morals all together. All have good reasons to be pissed at the others and all have their own major flaws. It gets very difficult to see anybody as a major villain because there is really no white or black. Though all sides are closer to the black on the gray scale. To fully lay out the rock-paper-scissors of insanity:
The Chantry and their affiliated Templar Order are simply executing its position of keeping mages in check, given that mages in this game have completely unpredictable degrees of power and are walking demon magnets. They do so by setting up their Circle (barracks for their Templar Order and a mage prison in all but name) in the former SLAVE PITS oh so quaintly named "The Gallows". The "alternative", in their opinion, is a fate like the Tevinter Imperium, which is ruled over by Magisters who thoroughly abuse their magic to stay in power.
The mages are rebelling against the overt cruelty of the Templars, seemingly worse in Kirkwall than anywhere else, up to and including making mages Tranquil for such things as talking about someone ELSE'S escape attempt. Of course, halfway through the game you learn about a significant mage rebellion in the works which, while in response to this abuse, is shown to be willing to sacrifice - sometimes literally - any number of innocents to achieve its goal.
The Qunari follow the Qun, a set of ideals wholly separate from every other nation. They are as confused by the way the "bas" (their term for non-Qun-followers, literally "things") run around all willy-nilly without a "purpose" in life: that "purpose" being a singular role assigned at birth with literally no deviation until you die. Even so much as wanting to retire from the life of a soldier is considered equivalent to heresy and treason rolled into one. They won't hesitate to kill if they feel it appropriate, but will also show respect to people with strong personal convictions. Act 2 ends with the Qunari holed up in Kirkwall getting fed up of the "chaos" around them and trying to take over... And very nearly succeeding.
Daein and Crimea engage in this for most of Fire Emblem: Radiant Dawn (taking it so far that you, the player, actually control a party from each country at different points, even when those two parties fight each other) before finally banding together against the unequivocally black morality of Begnion's corrupt senate.
When it comes to player races, World of Warcraft is surprisingly nuanced in terms of morality. Not only do all of the races indulge in truly unpleasant spin-off factions that can be killed by both sides, but you'll also find yourself accidentally doing unpleasant things for your allies, who often turn out to be sadists, murderers and major, MAJOR extremists who wipe out villages, torture prisoners and murder the innocent.
With hindsight, you've probably helped to destroy a few small and insignificant outposts yourself in the name of preventing further expansion.
In one example in the Stonetalon Mountains, you join Krom'Gar's army and work your way up through his ranks. He then murders some innocents and drops a nuke (kind of) on the land. He's executed, and you nearly get executed by Garrosh too for all the help you inadvertently gave him while questing eagerly for ranks. Whenever you realise that you've been helping a total psycho, it's something of an Oh, Crap moment.
This is actually a result of lore development. In the original Real-Time Strategy games, Warcraft was a pretty bog-standard Black and White Morality setup; you had the orcs, who were battle-crazed monsters who invaded from another world, and you had the humans, who were just trying to defend themselves from a surprise attack. In the second game, the orcs added the Dumb Muscle Ogres and the cannibalistic Hollywood Voodoo-practicing trolls to their armies, whilst humans forged a mutual defence pact with the peaceful elves, dwarves and gnomes. It wasn't until the third game that things became more morally complex, with the orcs being revealed as a once-peaceful, shamanistic race corrupted by dark magic and demonic influence into the monsters of prior games, and the Alliance being revealed as having thrown the surviving orcs into brutal internment camps after defeating them.
Battle for Wesnoth has this in the campaign Descent into Darkness. You control a young mage apprentice who takes up dark magic (read: animating corpses) to defend his town, and is exiled. His sister, the town guard, holy knights who show up for no reason but to piss you off in the hardest mission of the campaign all wish to have him killed. He takes revenge on them. In the end, it's mostly black versus black or black versus grey (with you playing the part of a very borderline black) but until they drop an anvil on you and have you fight endlessly repeating (and rather easy) battles against random commanders, you never genuinely know who to root for.
This is the theme of the Tales Series series. Ever since Phantasia, the seemingly vilest of antagonists has at minimum a lofty goal in mind, and the most noble of protagonists is either hiding something, misguided, or aiding and abetting someone who is either hiding something or misguided.
Symphonia: Mithos simply wanted to save the world from its own racist self by holding back progress and running "human ranches", and everything else he does is either for this for for Martel's sake. Lloyd's actions lead to much death and destruction as he changes the system, and Mithos's fears of technological abuse is proven right, as the next 4000 years between Symphonia and Phantasia can attest to.
Abyss: Van only wanted to Screw Destiny and destroy the Score, the near-mindless obedience of which has caused the destruction of his native Hod. Mohs is determined to follow it to the letter, believing it to be the Auldrant's only path to progress. On the heroes' side, Luke is a Jerkass extraordinaire, Tear keeps to herself all the time, Guy trusts Van, Jade was once a morally-ambiguous scientist, Anise is a gold-digger with good reason, and Natalia is revealed to be an adopted commoner. The only thing that kept Luke and company with A Lighter Shade of Grey is Character Development (especially Luke's traumatic transformation from Spoiled Brat to Nice Guy).
Vesperia: Alexei wanted to use Zaude to force the world to stop its reliance on blastia which is slowly killing it — unaware that it is actually the seal to an Eldritch Abomination. Yeager is an amoral mercenary who gives his earnings to an orphanage and has adopted two girls to be his sidecicks. On the heroes' side, Yuri is more than willing to stain his hands with blood in the name of justice, while Flynn believes in the power of law and order to the point of overlooking the basics of morality. As for the overarching plot, it comes down to a debate between preservation of nature at humanity's expense versus alteration of nature to suit human needs at expense of other lifeforms.
In Devil Survivor, it gets even more complicated. Agree to serve God, and you bring about world peace and freedom from sin by going Knight Templar on humanity and eradicating sin. Become the King of Demons, and you lead demonkind against God, but risk the annihilation of humanity should you be defeated. Or you can give the power of Bel to humanity as a whole, leading the world into a technological revolution powered by enslaved demons, or abandon the throne and return the world to normal. So long as you make a choice and don't shirk your responsibilities, no choice is the wrong one.
In the sequel, Deus Ex: Invisible War, while certain factions may come across as more or less positive, all have philosophies it's possible to sympathize with, while also being somewhat morally dubious. In the end you must pick between them, with no defined "good" or "bad" choice. You can also follow your own path and kill everybody, which backfires horribly (duh).
The prequel, Deus Ex: Human Revolution continues the tradition by asking you to side with one of three competing viewpoints regarding human augmentation and subsequently nudge the public interest in that direction... But you also get a fourth choice where you can refuse all of them and leave the world's to decide it's own fate (of course being a prequel to the first Deus Ex, the results are pretty much foregone no matter what you decide).
The three player factions (Humans, Mutants, and Biomeks) of Auto Assault were set up to be like this, but when you really look into it the Humans turn out to be the biggest bastards of the bunch, even if they were originally doing it to ensure their survival.
Command & Conquer started off with GDI as heroic good guys fighting against the evil Nod. However, later games revealed that Nod actually has reasons for fighting, and a number of the higher-ups in GDI are rather dodgy.
There's a major What the Hell, Player? moment in C&C 3, as if you're playing as GDI (the "good" guys), on the last mission you can choose to use a bomb that will kill hundreds of millions and destroy all of Europe. For this, the rational General who seemed like a pretty stand-up guy resigns in disgust, and the slimy politician (whose incompetence was all part of Kane's Plan) promotes you.
Ace Combat 5: The Unsung War features a war between Osea and Yuktobania… until it becomes known that the Belkans had been infiltrating high-ranking positions on both sides, essentially setting up a war of mutual destruction as vengeance for losing a previous war. By the end, both superpowers team up and collectively beat the tar out of the interlopers.
For Ace Combat Zero: The Belkan War, while the Belkans do not seem to have overt good going for them, Cipher can slide along the scale of greyness depending on how many crippled or civilian targets he goes after. A World With No Boundaries are Well-Intentioned Extremists who seek to bring about a One World Order and eliminate the political boundaries that lead to fighting... It's a pity they have to use a nuke to do so.
Attempting to lump any of those factions into anything resembling an alignment has more to do with the player's agreement with that faction's rhetoric than actual in-game observation. Example: Lady Deirdre Sky and the (supposedly) peace-loving tree huggers actually breeding and using said mind-raping worms as a military, or Chairman Yang really just promoting social harmony. Once you've played a game where Brother Lal (leader of the so-called "Pacifist" faction) or Lady Deirdre are that game's evil empire who starts dropping planet busters on you when you start picking apart their faction (a war which almost invariably occurs because -they- declared war on you for not giving in to their extortion demands), you begin to understand that Alpha Centauri truly does live this trope.
Indeed, every faction represents a rather broad philosophy on human kind, and every faction will use evil strategies particularly against a rising faction who's philosophy they see as evil. The Peacekeepers for instance favor diplomacy and democracy, so they're inevitably against you having any government (no matter how effective and moral) except democracy, and if you don't they're willing to massacre your people to change your regime by force. If you're not a police state, the Hive will be against you because they think religious states are stupid and that voting power in the hands of the weak masses leads to decadence, chaos and corruption. If you're not a theocratic state the Believers are against you. If you're not using the capitalist economic model Morgan Industries will think you're stifling economic progress and you need replacing. If you're not using a green economic model then the Gaians will treat you like you're exploiting and destroying the oh so pure environment and are evil. The Spartans will only respect people who value power and the University will only respect those who value knowledge. No matter what, some factions will dislike you and thus insult, harass, threaten, demand, and even attack you. You have to find deal with them one way or another. None of the core factions are necessarily bad, even the Hive can be very good for humanity, it's just a tightly controlled harsh parenting sort of good. Certain factions lend themselves better towards doing particular evil things because they get better bonuses (or less penalties) for those things, the Hive easily can and usually will default to wicked self interested tyranny rather than being some kind of ethical enlightened philosopher king. But even the most noble seeming factions can and will support their leader ordering outrageous and evil things, and they will be an asshole to you if you're not on their side. Even the most evil seeming factions, or the factions most dead set against you can be peacefully negotiated with, appeased and won over through multiple nonmilitary victory conditions.
The Star Wars: Knights of the Old Republic games break away from the typical Black and White Morality of the Force, especially in the second game, leading to plenty of Alternative Character Interpretation. On one hand, the Jedi, while trying to do the right thing, have a well-deserved reputation for being manipulative, closed-minded, and paralyzed with indecision in the face of crisis so soon after the previous one where they made a lot of mistakes. On the other, the Sith were led by a man who Jumped at the Call to protect the innocent, then (according to one untrustworthy source) "sacrificed himself" to the Dark Side and launched his own invasion as part of a master plan to provoke the Republic into preparing for some of the really evil things out there.
The Fable series plays with this Trope, especially with the character of Theresa. Played straight with Logan in the third game who, like Revan, became a vicious tyrant merely because he wanted to strength his country to fight The Crawler.
Depending on how you count, there have been between 7 and 12 playable factions in the five Geneforge games. All except Rawal and the Barzites can make a decent argument for themselves, and all except arguably the Awakened have Kicked The Dog at least once.
Xenosaga explicitly invokes this trope. Both The Federation and the Corrupt Church have a significant amount of innocent blood on their hands. Shion and her allies are frankly little different than Margulis' crew, all the Testaments believe they are bringing about a perfect universe for humanity, and Wilhelm manipulated all of history into a Stable Time Loop in order to keep the universe from dissipating entirely.
The companies Reliable Excavation and Demolition and Builder's League United in Team Fortress 2 are an interesting case - the motives and morality of both sides are identical. It isn't grey-on-grey, though because the motives and morality of both sides seem to be "World Domination", and "In The Gutter", respectively, making it black-on-black.
Considering the Evil Overlady announcer voice is identical for both sides, there is a potential possibility — later eventually confirmed by official tie-in comics — that both teams are working for the same boss.
Fallout: New Vegas has this, hard: The New California Republic are well-intentioned and filled with good people, but are ruthless expansionists, suffocated by bureaucracy and corruption, and would be spread way too thin to bring true safety to the Mojave Wasteland. Mr. House is genuine in his desire to rebuild lawful civilization and has the intelligence and resources to do so, but only cares about New Vegas and enforces his laws with an iron fist, ruthlessly executing anyone who opposes his rule. The Legion are a group of regressive, misogynistic and violent Slavers who are held together by one intelligent man, but are the only group capable of enforcing genuine security within the Mojave Wasteland and would actually be a boon to travelling merchants. The Wild Card route allows the Player Character to take over New Vegas themselves, but this requires the murder of Mr. House and there is nothing to indicate that they can succeed where the other factions would fail.
There's also the main struggle in the DLC "Honest Hearts" between New Canaanitesnote Mormons Daniel and Joshua Graham. Both are guardians of a relatively "innocent" tribe that is under attack by an old enemy of the New Canaanites. Daniel wants to withdraw the tribe to where their enemies cannot follow, out of guilt over the situation the New Canaanites have brought upon them. Graham wants to teach them to fight and destroy their enemies, both as a just thing to do and to assuage his own personal demons, of which there are many.
The Suikoden series, most notably Suikoden II, is praised for this trope, presenting the characters as humans in a compromising situation, instead of personifications of good or evil. It is very rare to find a hero who is completely morally sound (except possibly the main characters), yet it is also rare to find a villain who is purely and irredeemably evil (...except Luca Blight). While this keeps the stories from becoming too simple or cliche, it also gives an interesting human perspective to the bizarre and often supernatural happenings that occur.
In Yggdra Union, every major army is neither wholly good or evil — even the bandits are just taking advantage of others to survive, the Big Bad is a Well-Intentioned Extremist and a Woobie, Destroyer of Worlds, and the society that broke him so happens to be a bunch of Knight Templars being manipulated by a Villain with Good Publicity. The Royal Army, despite being the heroes, are not exempt from this — they commit several atrocities over the course of the game, just to hammer home the point that War Is Hell. The only unambiguously good character is Yggdra, the heroine, and even then she has severe naivety issues she has to work on.
Sigma Star Saga has this in spades: you, the heroic human character, are ordered to do some pretty horrible things by your superior, while the Krill, supposedly aliens hell-bent on Earth's destruction, are actually pretty decent people (with a few glaring exceptions) who harbor no particular ill will towards Earth at all. Turns out that there's a couple of Government Conspiracies on both sides of the conflict who are the truly evil ones, and the vast majority of both humans and Krill are good.
Ar tonelico II: Melody of Metafalica is a great example. Despite the fact that almost every character holds the same moral stance from beginning to end, pretty much every antagonist in the game will be considered a valuable ally at some point and nearly every ally gets a respectable stint as an antagonist. Even The Hero is arguably a Well-Intentioned Extremist, and the closest character to true evil is a foreigner trying to save his homeland.
The UNSC is fundamentally benevolent, but somewhat heavy-handed with its colonies, and willing to resort to questionable methods for survival. Up to and including the abduction, conditioning, and armament of the children of its own citizens, completely incognito of course.
The Insurrectionists had legitimate grievances with the authoritarian facets of the UNSC's administration of the colonies, but an extremist methodology, which includes nuking civilians, puts them squarely in the terrorist camp.
The Forerunners did mostly genuinely believe in the Mantle, their core ideology that revolved around protecting the galaxy and its inhabitants, but their technological superiority eventually turned them into arrogant, socially-stagnant imperialists who kept their client species weak and subservient, and when the Flood came knocking, they could ultimately only protect the galaxy by wiping out all unindexed life in the galaxy in a desperate last resort plan — which could be interpreted as a Heroic Sacrifice or the cost of their foolishness, depending on how idealistic/cynical one is.
The Flood had killed and infected trillions of people, but their leading hive mind, Gravemind, sincerely believes that he simply bring peace and prosperity to a galaxy which simply doesn't understand the Flood due to ignorance and fear ...though The Forerunner Saga muddles this somewhat into question by directly noting that the Flood were created in part to be a revenge against the Forerunners by their own Precursors.
Der Langrisser definitely falls into this trope. No matter what side you choose you'll end up fighting for peace while doing awful things in the way. There's no possible path that spares you the dramatic scene and the guilt of killing someone decent. You kill Vargas, who's just had a little daughter, and get to watch Leon tell his wife the sad news in the Light path, and you slaughter Scott and his father, in a rather cruel fashion in all others.
In the Dynasty Warriors series, despite the many changes in the story's overall tone over many games, one theme remains constant: no one faction is exclusively good or evil. Wei appears to be antagonistic, but Cao Cao is a pragmatic, Affably Evilchessmaster backed by warriors of laudable personal qualities. Shu is the nominally more heroic faction, but Liu Bei has done some things worth calling out, such as usurping his relative Liu Zhang Because Destiny Says So as well as his assault on Yi Ling, and Dynasty Warriors 7 in particular plays with Alternative Character Interpretation of his strategist/chancellor Zhuge Liang. Wu is the "opportunist" state which takes advantage of the chaos to do as it pleases, but their royal familynote father Sun Jian, sons Ce and Quan, and daughter Shangxiang is depicted as a tight-knit family backed by Sun Ce's sworn brother Zhou Yu and veterans from Sun Jian's days. Flaws aside, each kingdom has their fair share of heroic warriors. Even Zhang Jiao comes off pretty sympathetic, and in his ending he keeps his word in steering his new nation through the "Way of Peace". Even Dong Zhuo, the unambiguously evil Fat Bastard he is, is shown in his Campaign Mode to be desperately trying to salvage his rightful claim as Han emperor from the usurpers taking advantage of his realm's collapse. The Empires games take it a step further — you start out dead-center neutral with whoever you play as, and it's entirely up to you how good or evil your reign is. Of course, part of the reason is that, historically, none of the kingdoms succeeded in unifying China (that would be some last-minute Jin opportunist named Sima Yan), so it's impossible to say who the "hero" or "villain" really was.
Speaking of Dynasty Warriors, its Sengoku-themed sister franchise Samurai Warriors, especially the second title, also focuses on this at the battle of Sekigahara. Ishida Mitsunari's side portrays him as a Jerk with a Heart of Gold who tends to snark a lot but nevertheless believes in the value of friendship and honor, while showing his opponent Tokugawa Ieyasu as a Fat Bastard who wants to usurp the shogunate from Toyotomi Hideyori. Conversely, Tokugawa's side portrays him as A Father to His Men and a Reasonable Authority Figure, while accusing Mitsunari (especially his ally Naoe Kanetsugu) of hypocrisy, using the words "honor" and "justice" for unsavory ends and ultimately stealing people's freedom. In fact, Samurai Warriors is much grayer than Dynasty Warriors; the only more Obviously Evil character is Fuuma Kotarou, and even he's still grayer than Dong Zhuo.
MGS4. The Beauty & Beast Corps are war-scarred women outfitted with advanced nanotechnology and Liquid Ocelot is Good All Along (relatively), is actually the Ocelot from MGS3 pretending to have assimilated Liquid Snake's personality, and is stopping the Patriots' plans. On the good guys' side, Roy Campbell's marriage to Raiden's wife Rosemary was a facade meant to protect her and their supposedly-miscarried son Little John from the Patriots while Raiden is out fighting, and Rat Patrol 01 is the Patriots' Unwitting Pawns — their acronym ("RAT PT 01") can even be rearranged to spell "PATR10T" — who are meant to eliminate Ocelot before he foils their plans — they simply never expected Old Snake to destroy more than just Ocelot. It also turns out that the black-morality Solid Snake-era Patriots are nothing more but a faulty AI system developed by Zero long after he lost faith in humanity following Big Boss's departure, which deviated from the vision of Big Boss, Zero, SIGINT, Para-Medic, EVA and Ocelot — the original Patriots — and built an economy based on warfare, with Zero blissfully unaware (not to mention conveniently catatonic) of what he had wrought.
Ditto for the Legacy of Kain series. By the time Defiance rolls around, you're never really sure who's supposed to be the good guy and who the bad guy.
The Hylden have a single redeeming feature? Or are we just talking about freakish abominations not imprisoned in another universe?
Easy to believe that they were the victims until you realize that their genocide machine was in development before they got banished.
The Elder God is a real piece of work too. He's responsible for everything Nosgoth has suffered.
In Way of the Samurai, the player is often offered a spot on each and every side of whatever conflict happens to be occurring in the area he's found him/herself in.
In the first game, the choices given are to help the Kurou family, who, while admittedly driving an entire town out of their homes in order to sell the land to the government, are really only doing so to ensure their clan's future stability and who generally care about one another; the Akadama group, who are trying to overthrow the government to restore a caste system they pretty much know nothing about and who have no problem kidnapping and extorting to try and get their way, but who are bound by ties of honor and friendship and really are quite noble; and the remaining townsfolk, who are simply trying to survive, but who are willing to stoop to theft and opposition of government officials to achieve said goal. The only truly evil characters in the game are general Tamagawa, who has Chronic Backstabbing Disorder, and his ninja subordinate Hyuuma, who is pretty much just a jerk because he can be.
The second has even more moral ambiguity. We're given the choice between the Aotou Gang, who are run by an Obviously EvilJerk Ass but whose rank and file are shown to be likable fellows who are easily swayed; the town magistrates, who act like Knights Templar, but truly love their town; and the town militia, who are the working stiffs just trying to live their lives, but who are also involved with prostitution and minor drug dealing. On the other hand, Kyojiro Kagenuma really IS as insane and just plain evil as she appears to be. That she has her own ending (and it's a major Kick the Dog one) is telltale.
Final Fantasy XII. To elaborate, on the villain's side we have the machivellian, Affably EvilPrince who wants to become the emperor and restore order to the empire, the Well-Intentioned ExtremistMad Scientist who's working with his demigod Spirit Advisor to overthrow the Jerkass Gods, the Judges who bar one are well-intentioned tools devoted to protecting to law, and the Emperor himself who is trying to keep the Senate from turning his youngest son into a puppet heir while preventing the empire from collapsing into civil war. On the good guys side we have a vengeful, stubborn princess who will stop at nothing (including genocide) to regain her kingdom and pay back the empire for her dead husband, and who nearly becomes the willing puppet of the aforementioned Jerkass Gods to achieve this, a pair of sky pirates who are just in it for the treasure (and one of them knows exactly what the princess is trying to do and where it would lead), an old soldier who's willing to do anything to protect the princess, and finally two slightly naive teenagers, one of whom is a petty thief. In between this lot we have a Marquis-cum-Resistance leader who plays permanent double agent and who's loyalties depend on who is winning, a Rebel general who's willing to sell out his own princess if it means his country will be restored even if it's in name only, an ex-Judge who destroyed an entire city and now resorts to piracy to make up for his sins, and an imperial prince who is caught between caution and preemptive assault in the protection of his nation. The only good character is really the youngest prince, and he suffers from a bad case of naivety and idealism.
The Assassin's Creed series makes this very clear. While the Assassins are made out to be selfless shadow figure heroes of the people and the Templars the evildoers of the world, it would be more accurate to say both parties seek for a world of peace and prosperity, they just apply different methods.
From nearly everything we've seen of the established Assassins and Templars, it's plainly obvious that the Assassins have admirable goals (promote the arts, protect free speech, replace myth with scientific knowledge, etc.), while the Templars are at best petty tyrants. Where the gray creeps in (and drives the series) is their attitudes toward humanity at large. The Templars think that the pitiful masses are too ignorant and foolish to be trusted with freedom, and, evil or not, it would be better for the world if they were enslaved (and you certainly can make a case for that). The Assassins think that freedom should be protected at all costs, even if it ends up hurting humanity (and you can make a case for that as well). As of Revelations, it remains to be seen which side is right...which is just how UbiSoft likes it.
The historical backdrops as well. UbiSoft make a big point of presenting all sides as sympathetically and flawed as possible while still maintaining historical accuracy. For the third game, which is set in The American Revolution, UbiSoft have made it very clear to depict the war as this, in the face of widespread criticism. The British of course have their share of Evil Brits and atrocities, but want to hold their empire together more than anything else, while it's made very clear that the Colonials want freedom, but don't really care for Connor's freedom, and in fact Connor points out the hypocrisy of wanting freedom while owning slaves. Then there's George Washington destroying several native villages, including Connor's home village, which is Truth in Television.
The third game introduces a bit of 'Black' into the mix: Juno, who manipulated Assassins and Templars alike to bring about her own resurrection so she could conquer humanity.
On one side is Emperor Cole (a.k.a. Tyrant) and his underlings whose philosophy is something like, "Order at any cost." If the player joins the Loyalists, he can then use the power of the Praetorian Empire to either protect its citizens or advance his personal power.
On the other side is the underground Resistance whose creed is "Freedom at any cost." If the player joins them, he can either work to free the people of Praetoria or can act as agent of chaos.
Infinite Space has several instances of this, although nothing in the game tops the long-running conflict between Kalymnos and Nova Nacio. This is especially apparent during the Irvest Sector War, with the so-called People Committee of Kalymnos attempts to obliterate the residents of an entire planet owned by Nova Nacio by crashing its satellite to win the war, while Nova Nacio has been secretly developing a very powerful weapon on the same planet under the cover of colonization project.
During the stealth tutorial for Splinter Cell: Chaos Theory, Sam Fisher lampshades this trope:
Enemy soldiers? They're not my enemy; they're just doing their jobs. Light is the real enemy.
Final Fantasy Tactics. In the beginning, two princes are fighting each other for the throne. Since it is basically the War of the Roses in the form of Final Fantasy, neither side is really good. Later in the game it becomes more like Black and Gray Morality once the Church and Delita start playing more significant roles in the war. Delita, while ultimately a hero that saves the kingdom from falling into utter chaos, still uses any and every Machiavellian method available to him in order to accomplish his goals. The Church is basically controlled by Satan. The only white to be found is Ramza and his fate is to become a footnote in history.
Used heavily in the Golden Sun games, though it doesn't quite become apparent until The Lost Age, where all the antagonists of The Broken Seal are revealed to have been working for good ends, and trying to defy a system that if left in place will result in the decline and ultimate end of the world of Weyard, but whose supporters (rightly) fear the abuse of Alchemy unleashed.
Really, there is only one truly evil character in the whole series. Too bad that he's The Chessmaster... And even then, Alex isn't exactly evil, just self serving. He manipulates to his own ends, but he never shows any actual malice towards the characters. The only time he ever struck against a character was when they attacked him, and it was only to stop their attack.
The moment that time travel gets involved at the end of the respective factions' intro zones, who's "right" and "wrong" goes out the window. The Guardians are rightly angry at the Defiants for (inadvertently) siding with the Big Bad and using technology that drains the power of the Veil, the only thing holding back a massive invasion of the Elemental Planes and forces of the Dragons. After the initial wave is stopped and the PC is thrown forward in time, the Guardians spend the next X years throwing everything they have into a genocidal war against the Defiants, instead of working WITH them to stop the forces of the Dragons. Because of this, any hope they had of using Defiant technology to fix what it broke in the first place is lost, leading to the Defiant intro happening right at the climax of The End of the World as We Know It, and you get to time-travel back to stop it from happening. Upon returning back and delivering news of what's to come, and the schematics of technology that can stop it, the Defiant leaders try and figure out how to use the tech to finally defeat the Guardians, and deal with the planar invasions later.
Wings portrays the Allied perspective on WW1 if you play as them, or the German perspective if you play as them, but doesn't seem to take sides overall.
None of the three main factions in Sins of a Solar Empire can be considered truly good or bad. The Trade Emergency Coalition appear to be just Technical Pacifists trying to fight off the "evil" Vasari and the vengeful Advent, but the reason the Advent are vengeful is because the traders exiled them from their homeworld 1000 years before for having different ideas about social norms. The Advent may have legitimate grievances against the traders, except the ones who actually exiled them died a long time ago, so they're trying to punish people who didn't do anything to them. The Vasari used to be a vast empire and still follow similar policies in terms of enslavement and locking down colonies, but they're just the remains from a single colony that have been fleeing an unknown enemy that has destroyed the rest of the empire for tens of thousands of years and are conquering trader worlds only to get enough resources to be able to continue their flight.
All three sides engage in a total war against their enemies, nuking planets from orbit until everyone is dead.
Might and Magic VIII is full of this: it features a Big Bad whose only reason for being that is that he can't stop once he has started (no matter how much he wants to)note He was programmed that way as a security measure, to keep the Kreegans from subverting him, a conflict between dragon hunters out for profit and xenophobic dragons that see nothing wrong with eating other sentients, and a war between the Necromancers' Guild of Jadame (who, in the modern day of the game, are a fairly laid-back bunch, mostly wanting to keep to themselves) and the Church of the Sun (who came to Jadame to wage war on Necromancers without provocation, and are somewhat corrupt and self-serving).
In Avadon, both Redbeard and the Duke have both positive and negative traits that can make it hard to decide who to side with.
In Dark Souls, the central conflict in the game is extremely lacking in details, but what details we do know ultimately make it an example of this.
PlanetSide. Three factions endlessly fighting over a tiny ball of rock god-know-where chuck full of alien technology, using respawning technology to keep the war going. The Terran Republic established a thousand years of peace on Earth - while sacrificing freedom. The New Conglomerate rebelled for more personal freedom, but they are backed by by large corporations and mercenaries). The Vanu Sovereignty wants to uplift humanity to the status of the ancient Vanu - but possibly at the cost of your identity and freedom.
Alien vs. Predator: While the leaders of that big corporation are a bunch of greedy assholes, most of the employees are just people doing their work or innocent victims who haven't done anything bad. The marines are usually well-meaning if slightly hardballed with their work. The Xenomorphs are obviously nasty bastards but in the video games, it's their territories that are being invaded and their queen violated, so in all rights they're fighting an war of self-defence against the humans and the yautjas, thought with rules that aren't exactly what the Geneva Conventions would allow. The Yautjas no doubt starts wars and deaths for no actual good reason but they do have standards on which things the hunters are allowed to kill; women, children, sick and old are forbidden to hunt but for the rest, it's a free game with whatever nasty and violent way they want to use.
The Last of Us features a lot throughout the course of the game. The trailer even has Ellie say, "You either hang onto your morals and die or do whatever it takes to survive."
The end has a large conflict featuring Ellie. Marlene planned to use Ellie to create a vaccine to cure the Infected, which would ultimately result in her dying. Joel, because he saw her as another daughter, saves her before the Fireflies perform the surgery, thus wasting the chance to save the human race.
Supreme Commander. All sides have sympathetic ideals, if not necessarily ideal means to practice them, and are composed of a mix of fundamentally good people who follow those ideals, and bad people who ignore them. The narrative doesn't seem to really take any sides either. Your choices are a) a human Racial Remnant that wants to rebuild the old Earth empire and reassert humanity as the leaders of the galaxy no matter what, but are depicted as the universe's Only Sane Man, b) an aggressive religious movement that fights to achieve peace and harmony and is led by a kindly Messianic Archetype, or c) a La Résistance movement for oppressed cyborgs that employs questionable methods but fights for freedom nonetheless.
At Freelancer most factions except the Xenos (who are obvious xenophobic omnicidal maniacs) and the Liberty Police (defending the land of freedom and whatnot) are somewhat guilty of this, ranging from farmers turned into terrorists, tree-huggers turned into terrorists and hackers turned into terrorists to tyrannical and corrupt regimes and corporations that would sell their mothers for money -and eventually causing said mothers to go terrorist-. Special mention goes to the Corsairs and Outcasts faction, whose mothership lost contact with the others during travel, forcing them to go outlaw in a way or the other, and the other factions subsequentially shoot upon them. Apparently diplomacy is an unknown concept to this universe.
In spite of the very clear divide painted in the promotional material, neither of the factions in WildStar are not entirely good nor evil. The Exile "heroes" are basically criminals and terrorists, and sink to some serious lows to have a fighting chance, the Dominion "villains" provide a highly tolerant, well-educated, and prosperous and free society to their citizens.
In Papers, Please, there are virtually no "right" or "wrong" decisions. Over the course of the game, you'll have to face ethical dilemmas whether or not you should obey the rules or sympathize with the entrant. Heck, even the border guards and your supervisor will make requests that is considered to be morally grey in the eyes of the player. Thus, this is why the game has Multiple Endings.
Daggerfall is full of this. About the only morally unambiguous choice in the end-game is to aid the Underking, and then only because his goal is to finally die rather than to actually use Numidium. There are several candidates for Complete Monster, and you will aid at least one of them out of your own free will, without being fooled, over the course of the main storyline. A note on Daggerfall: it turns out that due to an event called a "Dragon Break", in which time flows in a non-linear fashion, somehow all the choices you're able to make ended up happening at the exact same time. This would be known as the "Warp in the West", and resulted in having every single nation in western Tamriel (there were a lot) turn into two provinces and swear loyalty to the Empire.
Morrowind. Although the main quest is pretty much black-and-white, the politics in Vvardenfell are very clearly Gray And Gray. House Hlaalu, for example, is open-minded but corrupted, House Telvanni is honest but elitist, House Redoran is strong but xenophobic, the Empire often ranges from oppressive to a little bit too lax, the Dunmer Temple is kind and charitable but has Knights Templar (the Ordinators) and is to some degree a Corrupt Church, and the three god-kings to which it is devoted are respectively benevolent but pathologically dishonest, egotistically psychotic, and dead. House Dagoth are portrayed as evil, but still remain somewhat gray. At most the main quest is closer to Black and Gray Morality.
The fifth installment, Skyrim, takes place in the middle of a civil war: the Empire, after losing a war against the AldmeriDominion, was forced to outlaw the worship of Talos and are generally viewed as cowards who oppress the citizens of Skyrim instead of resisting the Dominion's rule. The Stormcloak Rebellion wants an independent kingdom, but they're also ultranationalists who dangerously border outright racism and confine the Argonians, Khajiit and Dark Elves to slums. In the defense of that last point, the Argonians and Dunmer are ancestral enemies (indeed, the former recently conquered the homeland of the latter, and the latter was enslaving the former for generations), so their desire to keep the Argonians and Dunmer apart may be in the interests of preventing a race war in their capital.
In the Fallout 3 DLC "The Pitt", the two factions the Lone Wanderer encounters fit this trope. Wernher, leader of the slave rebellion, wants to steal the cure to the mutations that ravage The Pitt to use it as a bargaining chip for the slaves' freedom. Ashur, ruler of the Pitt, considers his Raider army and slave workforce necessary evils that gave The Pitt safety and industrial power; he hopes to use the drug to cure his constituents (a cure taken from his own daughter, who was born immune to the radiation), allowing them to bear healthy children which would grow to eventually replace slave labor because with a homegrown workforce. The player can side with either faction.
Many of the multiplayer characters are, according to their back-stories, either greedy sellswords or criminals.
Throne claimants each have their own backstory about why they should be king/queen. The current monarchs will actually have their own sides to the story and their own reasons, so you're left to decide who's story is worth more. For example, Arwa the Pearled One of the Sarranid Sultanate claims that Sultan Hakim is an Evil Uncle who illegally usurped the throne from her, but Sultan Hakim counters that she is a Bitch in Sheep's Clothing, and that he has a more legitimate claim due to his royal heritage (while Arwa is an adopted peasant girl). The only claimant/monarch conflict where one side is definitely more sympathetic than the other is Swadia, which pits the competent and reasonable Lady Isolla against the incompetent and tyrannical King Harlaus; really, when you ask for Harlaus' reason for exiling Isolla and denying her claim, his argument basically amounts to "she is a woman and therefore won't rule well".
Believe it or not, Mario's world was like this in his debut game. In the arcade Donkey Kong, Mario had captured the eponymous ape and wasn't very nice to him, leading to DK escaping and abducting Mario's girlfriend as revenge by proxy. Nintendo of America workers even named Mario after their landlord as a result of being mad at him, which backfired in a truly epic fashion. However, while Mario did mistreat Donkey Kong, he did risk life and limb to save Pauline from the rampaging ape, so he was more of a JerkassAnti-Hero than a Villain Protagonist. On the other side of the conflict while Donkey Kong did kidnap Pauline and needlessly harassed Stanley in the third game, he's shown to have had a loving son who rescued him from Mario in the sequel.
Last Res0rt, with several condemned criminals in its ranks, usually sits firmly here; while most of the characters involved are criminals (and even some of the volunteers are only a couple notches above 'em), it's only when Arikos, Geisha, or the Celeste get involved that the comic slips into Black and Gray Morality.
Angels 2200 does not go into the causes behind the colonies' revolt against earth, and both sides are composed of leaders who use morally dubious tactics in order to win and soldiers who only want to stay alive. Then again, depending on what the true origin of the genetic plague is, one of the sides might count as black.
Word of God claims that this is the case in Drowtales, where the story is shown through several viewpoint characters, neither being portrayed as good/evil and with fairly realistic motivations for their actions. It also features a character who in most stories would be a shoe in for The Hero who is a horrifically abusive parent, while her counterpart on the "bad" side is unquestionably one of the best parents in the series. And even the character who so far seems to be clearest example of the Big Bad sill remains somewhat sympathetic and has a point on some issues.
In the very Not Safe for Work webcomic Felarya, man - eating monsters are depicted as no worse than the humans they eat.
The conflict between Agatha and Klaus in Girl Genius. Klaus has every reason to want to keep Agatha locked up until she's proven trustworthy, and (given recent events) can make a pretty good case for killing her with fire. On the other hand, Agatha really hasn't done much to deserve that (yet), aside from getting the Big Bad stuck in her head, and she's got every right to fight back (particularly when her friends get caught in the crossfire). Not forgetting Othar, who is killing off sparks. He's deluded, but considering somespark'screations he's kinda right.
Othar slips out of grey if you read the side materials in his point of view: his solution to the problems caused by Sparks is to kill them all. He's pretty OK with a train going into a canyon with everybody aboard when he finds out they're all Sparks. Let's hope he never realizes the definite possibility that he will have to kill all humans to permanently eliminate Sparks.
Klaus' reign over Europa itself. At first, it's pretty much implied to be an Evil Empire, with Klaus at its head as the Big Bad and his son as the main love interest for the protagonist. Then you read about his backstory and what Europa was like before Klaus: note There were several years in which Klaus and the heroic Heterodyne Boys roamed Europa as adventurers. Before the Boys, the Heterodynes were actually very brutal, very sadistic mad scientists with no regard for human life and a massive army of fiercely loyal superhumans at their disposal. The idyllic times of the Boys ended when one of their wives, who was cheating on her husband with Klaus, drugged the latter after a tryst and presumably abandoned him in a place he would be hard-pressed to ever return from. Then she engineered a series of events that led to the disappearance of the Boys, the orphaning of her daughter, and the total destruction of peace around all Europa, earning her the nickname The Other. By the time of Klaus' return, he has almost no choice but to engage in the most brutal methods possible in order to make the region livable again, including usurping power from every noble imaginable by taking their heirs as hostages. It takes this and an internal betrayal within The Other's faction in order to bring Europa some stability. When The Other's return nearly two decades later sets off a chain of events resulting in both Klaus and Agatha being put out of commission for a while, Europa degrades right back to chaos, and that's with most of the rebelling factions banding together to support the new Baron - showing just how necessary the previous Baron's ruthlessness really was.
The main conflict in Juathuur is between control and freedom. Both sides have their reasons, and their differences are mainly due to age gaps (as the 'control' side grew up in a world torn by war, and the 'freedom' side did not). See the comic page for details.
The main characters of Narbonic are a mad scientist, her henchwoman who loves to destroy things, her henchman with a deep dark secret not even he knows, and a superintelligent gerbil whose efforts to do good often cause more havoc and chaos than some of the evil plans afoot.
The Kingfisher: Both Theodore and his sworn enemies - the vampire progenitors - are uncanny, manipulative, and monstrous. It's telling that the protagonist has not committed to a side.
Lackadaisy is full of this. Even the Spoiled Sweet, pretty girl who mainly works the restaurant front knows how to use a gun, is still a pretty big part in the operation, and in a recent arc, is still responsible for a large shipment of booze going to Lackadaisy. Basically, nobody in the comic is blameless, and it reaches truly ridiculous heights in the more recent arcs.
In Off-White, the dark wolf spirit Hati is trying to save the world, but he's willing to kill (or at least threaten to kill) Sköll/Ike's innocent pack mates to do so. Meanwhile, the white wolf spirit Sköll wants the world to die, but the world is going to get rotten anyway because the guardian of good died so goodness is dying with her.
The Forever War between Angels and Demons in Slightly Damned. Neither species is inherently good or evil, and both have committed atrocities, as you might expect in a war that long.
In Terra the Forever War between the United Earth Coalition and Asurian Empire is a fairly dark version. Both sides are responsible for atrocities, and both sides also have good people who are just Punch Clock Villains (one of the main characters joined the UEC military to feed his family, not out of ideology). The Resistance is A Lighter Shade of Grey: they're fighting for their homes and loved ones and have the goal of forcing both sides to the negotiating table with the hopes of ending the war and setting up a Fictional United Nations, but they use assassination as a primary tactic.
Erfworld is centered around the conflict between Gobwin Knob and the Royal Crown Coalition led by Jetstone. Gobwin Knob is led by Stanley who is convinced he is following the will of the Titans and many of his subordinates are merely trying to survive against their enemies. The members of the RCC have good reason to try to put down Stanley, as he's been attacking most of them in his quest to get the Arkentools. Jetstone, however, doesn't really have a reason to hate Stanley beyond the fact that he isn't a Royal, which they believe to be the only proper rulers in Erfworld. Even so, they still value honor and justice in battle, which Stanley and his Chief Warlord Parson don't. The whole thing is further muddied by the very nature of Erfworld, where open warfare against someone is virtually the only way to survive, much less grow, and the local laws of physics promote a forever war.
Draconia Chronicles: Originally, the central conflict had the Tigers as the clear good guys and the Dragons as the clear bad guys. However, with the addition of some sympathetic Dragon characters, and some brutal Kick the Dog moments for the Tiger side, the conflict instead falls squarely into this.
Cucumber Quest is a more light-hearted variation of this. Characters like Cordelia and the Disaster Masters are pretty Obviously Evil and they don't exactly try to hide it...but their actual interactions with other members of the cast can be surprisingly heartwarming such as Cordelia cheering up her minion Peridot as well as Noisemaster and Mutemaster's unseparable friendship. Meanwhile on the "heroes" side, the Dream Oracle, the supposed Big Good, is portrayed as hilariously incompetent at her job and even interrupts the chapter intermissions whenever they start to question her actions, while Cucumber's father Cabbage is pretty much the personification of a Jerkface, being greedy and teaching his son to do well on tests by cheating. Most of the time it's Played for Laughs.
Homestuck has the conflict between Prospit and Derse, the conflict that drives the "game" of Sburb. Prospit is fighting so that Sburb can perform it's intended purpose, creating new universes, while Derse is fighting to destroy Skaia, which would stop Sburb from destroying innocent worlds and races to propagate itself. In-Universe the players of Sburb are intended to side with Prospit and thus continue the game but it's made clear to the reader that both sides of the conflict are mostly good people. Indeed, late in the Kids session the two armies end up making peace under the unified goal of overthrowing the Black King though this doesn't end well due to Bec Noir...
Schlock Mercenary falls into this quite hard. The main characters are mercenaries who will enthusiastically participate in almost anything as long as there's money in it, while the governments they work for scratch and claw for advantage. Even the most benevolent figure, the Fleetmind, is still extremely ruthless when it needs to be. At the same time, however, most of the people engaging in active bastardry are there for positive reasons such as patriotism, they're just working towards them in horrible, horrible ways.
The online book Imperial Dawn is centered around a war between those who support democracy, and those who are moving towards an arguably better new government system. Neither side is presented as wholly good nor bad.
There Will Be Brawl: There is no good or evil. The 'good guys' are drug dealers, strippers, or Fallen Heroes, the 'bad guys' actually have a plan to improve the quality of life in the Mushroom Kingdom, and the cops are corrupt and trying to usurp the throne. The only one with a clear designation is Kirby...who is a psychotic cannibal, a la Hannibal Lecter.
There's also Red, the only character who is truly good. Which makes it all the more sad (and fitting) when he dies by Pikmin bomb
Red vs. Blue. The default characterization seems to be 'incompetent jerk', with variations lying mostly in the type and degree of incompetence and/or jerkassery.
The gray becomes even more clear when the Freelancer backstory starts to be brought out in seasons 6 through 10. On one hand, you want to root for the Freelancers. On the other, they're doing a lot of morally questionable things. Even those who are clearly "bad guys" (Sigma, the Director, CT, etc.) have a lot of nuance once you learn why they do the horrible things they do, and in the end, it's hard to say who's really good or bad.
"Champions of Meridell" in Neopets is the first war between Meridell and the Darigan Citadel, after the greedy king Skarl stole the orb of prosperity from the originally Perfect Pacifist People of Darigan for his own glory and power, causing them much misery and pain and mutating them into vengeful monsters who try to destroy Meridell. There are both good and evil in both sides, with the heroic Jeran serving the villainous Skarl, and the anti-villain Darigan seeking to return the orb to his people.
In Pokegirls, humankind survives entirely due to a system of raping and brainwashing the eponymous female subspecies... which are themselves notorious for rape and murder.
While Doug's writings of the anniversaries are a bit blacker, The Nostalgia Critic's show runs on this. Critic's a Psychopathic Manchild but tries to be a decent human being, Sage-as-Satan is much less scary than he is as his normal self in other series, Big Good Santa Christ can hold a mean grudge and even major troll Douchey manages to show a bit of heart when he feels pity for Critic at the end of the third fuck-up list.
Comes up in RWBY, and Played for Drama. What happens when you take two people who are supposed to be friends and colleagues and have circumstances beyond their control place them on opposite sides of a conflict like this? Just ask Weiss and Blake. Weiss is the heiress of the Schnee Dust Company, and Blake is a former member of the White Fang terrorist group. Weiss and her family have been targeted by members of the White Fang for as long as she can remember, and it's also implied that her ill-tempered father took his frustrations out on her, but where Weiss is wrong is that her personal prejudices cross the boundaries onto all Faunas in general. While it is true that Blake was a member of the White Fang, she left because they began terrorising and killing innocent people, which she objected to. Despite this, she still feels compelled to defend their cause and their actions. Of the two, Blake is perhaps the more sympathetic, but Weiss remains a Tragic Bigot.
In Space Janitors, a parody of the Star Wars universe, rebels are portrayed as egotistical adrenaline junkies. Meanwhile, imperial citizen are portrayed as very happy to completely buy into the propaganda of the empire.
Justice League Unlimited: For the Cadmus Story Arc, Cadmus is presented as rather dodgy, but with legitimate fears about the dangers of superheroes. The heroes, meanwhile, had a habit of putting the good of their own members ahead of that of unpowered individuals most at risk of supervillains. Notably, this went so far that the writers were forced to have a more 'traditional' supervillain take over the Big Bad seat, because they had no way to finish the arc in a satisfactory way with the time given without massive Motive Decay to make Cadmus arbitrarily 'evil'.
Exo Squad. The Neosapiens do perform atrocities and Phaeton is pretty much a Card-Carrying Villain but they are responding to being essentially slaves whose earlier, more moderate attempt to gain civil rights was stomped on. The Space Pirates are more chaotic than evil and are motivated by a combination of survival and having been screwed over themselves in the past. The Space Pirates were a prison labor force that were abandoned once the Neo Sapiens were made and were driven crazy by their secret homeworld Chaos.
Tom and Jerry. Though Tom is often out to harass, kill, and eat Jerry, you can't overlook the fact that Jerry is extremely sadistic, and sometimes isn't even provoked. But that still doesn't excuse Tom, who often brings his punishment upon himself, and at the beginning of the majority of the episodes is bullying Jerry. At times its hard to tell who the victim is; sometimes its neither (and occasionally it's both).
The Jet/Zuko conflict in the later half of season 2 of Avatar: The Last Airbender, since both are former villains seemingly on the road to redemption, there's really no way to give one moral superiority. However, since Jet was the aggressor, and the show had spent most of the season building up Zuko's eventual Heel-Face Turn, he came off as more in the right.
The Sequel Series, The Legend of Korra, is even better at this. The main enemies are the Equalists, who show Fantastic Racism towards bending and wish to eradicate it, and their leader Amon can be very brutal and callous in his treatment of benders. On the other hand, he has a point - the Council of Republic City is itself very prejudiced towards non-benders, and only Tenzin appears to represent their best interests as well as those of benders. There are good and bad people on both sides - Tarrlok vs. Tenzin on the council, and Amon's side has people like Hiroshi Sato, who despises benders for similar reasons but is still more sympathetic than the Big Bad. On a non-political level, Korra and her friends aren't depicted as paragons of goodness (though they try to do what's right), and even characters like Tahno and Lin Beifong have multiple dimensions to their personalities. Only Tenzin's family can be considered purely "white", while Yakone and his son Tarrlokmight well be purely "black".
Ed, Edd n Eddy is chock full of this. Kevin is evil in the eyes of Eddy, who is actually pretty cruel himself, who is viewed as merely ignorant by Double-D, who is seen as a talking encyclopedia to Ed, who is seen as a complete idiot by Sarah, who is seen as the greatest heroine by Jimmy, but is otherwise seen as an annoying and violent Scrappy by everyone else. And that's not even covering the entire cast.
Daria: Despite some of the shallow natures and flaws of characters, few characters are truly malicious and at some points prove to be decent people (such as DeMartino and Britney). Daria, while mostly moral, can often become petty and cold towards others.
Regular Show: Mordecai and Rigby are far from good workers most of the time, and often either slack off, or inadvertently cause destruction. However, their boss Benson is also a Jerkass who shows blatant favoritism towards other workers, and occasionally deliberately antagonizes the main duo, but his boss is even worse then him.
Pretty much the central conflict of Ćon Flux. Aeon is a ruthless self-motivated secret agent doing spy-work for an underground organisation, or possibly simple sabotage for the sake of anarchy, but she honestly thinks her terrorist activities are done for the greater good. Trevor is a morally ambiguous totalitarian ruler who genuinely believes that people are better off submitting to his authority. May also count as Blue and Orange Morality; the two take their opposite ideologies to such extremes that they're difficult to quantify by realistic standards.