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- It's difficult for Soul Eater fans to believe that the series used to be a comedy. Inclusions of Mind Rape, actual rape, deals with the voice in your head, etc aside, the most triumphant example of this would have to be the point in the series where the Grim Reaper decides to wipe out a whole town because the Kishin just might be hiding there. Eventually the Kishin could wipe out the whole world, but the situation at just halfway through the story is that dire.
- One Piece started out as a story about a cheerful crew of good-natured pirates who fight other, more hostile pirates and a corrupt government. A little before halfway through the story, however, we start seeing absolutely ruthless fellow pirates who demonstrate why normal people fear that word, as well as government people who genuinely have the best intentions for the populace at large. The backstory of Luffy, the protagonist, comes up around this point in the series and strongly hints that he fights the government not out of a sense of justice, but for personal revenge, totally unbeknownst to his crewmates. Meanwhile, some key people from the military have defected while some notable pirates seen before have allied with the government, each for their own reasons. Finally, there is a growing notion that this government only appears to do evil actions to prevent superweapons with the ability to destroy the entire planet from falling into the hands of those who actually want to use it, most of whom are pirates, many of them acquaintances of Luffy. At this point, there are good and bad people on both sides and plenty of hard decisions people with power and/or fame must make.
- The Universal Century continuity of Gundam underwent this as more series are written. The original Mobile Suit Gundam was light-gray versus black, with the Earth Federation being a well-intentioned government led by responsible people fighting against space Nazis, even though there were heroes on both sides and a few blemishes on the Federation. As the series became more developed, the Federation became increasingly portrayed as a corrupt and incompetent institution that inevitably becomes a tool of the villains, requiring heroes (who are often rather deeply flawed individuals themselves) to mutiny against the Federation to set it right. The various Zeonic movements remain consistently evil, though their leaders are often more sympathetic than the Hitler-idolizing Gihren Zabi.
- In Why Am I Crying, Scootaloo believes that Diamond Tiara and all bullies were born pure evil and that they were incapable of changing their ways. As the story goes on, Scootaloo finds out that Diamond Tiara had a Hidden Heart of Gold and that her kindhearted teacher Miss Cheerilee was a horrible bully in her high school days, and she soon realizes that bullies can change for the better.
- The first Star Wars trilogy (IV-VI) had this. A New Hope was like a comic book, with mostly clear-cut heroes and villains (except for Lovable Rogue Han Solo). In The Empire Strikes Back, we learn that Obi-Wan lied to Luke about his father, leading to Return of the Jedi where Luke is told that he must kill his own father or the Emperor will win. The prequels end up being much greyer than the originals, with the heroes using Child Soldiers and a slave army.
- The expanded universe runs the whole gamut. The first few novels are fairly light, only for subsequent ones to get darker. Then every couple of series there'll be a conscious effort to be lighter again, which in turn get darker etc etc.
- Pirates of the Caribbean already starts off as Gray and Black Morality, but includes distinctly white characters such as Will Turner and Elizabeth Swann. These characters gain shades of gray throughout the second and third movies. On the opposite side of the spectrum is Barbossa, who was mostly black in the first film but is just as gray as the other protagonists after his resurrection by Tia Dalma.
- The Captain America movies in the Marvel Cinematic Universe received this treatment especially hard. The first movie, The First Avenger starts off as a straightforward Black and White Morality World War II period flick with the title character fighting HYDRA — A Nazi by Any Other Name. The first sequel, The Winter Soldier has the hero fighting the spy agency S.H.I.E.L.D. that was infiltrated by HYDRA ever since its creation but the antagonist raise valid points about security vs. free will in a world of superheroes. Come to full blown in the third movie, Civil War, the antagonist this time is Steve's own former Avengers teammates and the government over whether or not superheroes should work with the government, making it cross right into Gray and Grey Morality.
- Animorphs starts off as a typical children's sci-fi with the Yeerks as evil and the Animorphs, and by extension the Andalites, as the good guys. This doesn't stick. Specifically, while some characters (Visser Three and Crayak stand out) are introduced at and stay firmly in "evil" territory, the Yeerks as a whole are revealed to be a nuanced race with a sizable peace faction, the Andalites are elitist and in some ways only barely better than the Yeerks, and the Animorphs have to go seriously grey before all is said and done.
- The Saga of Darren Shan series developed along these lines due to the Character Development of the protagonist and narrator. While most of the adult vampires would admit that there was some good in themselves and the rival vampaneze, the story is told form Darren's point of view. The effect was that the act of taking blood went from a horrifying abuse of other people to everyday routine, vampire culture went from rigid and savage to traditional but noble, and even the Vampaneze, a branch of vampires who serve as the main antagonists, killing every time they had to drink blood and killing several of Darren's friends, went from being regarded as monsters to seen with a respect almost similar to that between diffrent countries or rival political parties.
- Karen A. Brush's children's book The Pig, The Prince, and the Unicorn begins as a classic Good vs. Evil Quest story, but as the naive protagonist (the titular Pig) finds out more and more about the opposing side as he journeys, at the end of his quest he's totally conflicted about whether to go through with it or not.
- The Sword of Truth is an inversion. It starts out with a deep discussion of good and evil, right and wrong, and cause-and-effect, including black, white, and lots of distinct shades of grey. As the focus of the series switched to the war against the Imperial Order, it became a very us-against-them, black-and-white morality environment, to the point where the protagonists were doing things at the end of the series that they would have decried as evil at the beginning.
- The Honor Harrington series started out reasonably black-and-white, with the Star Kingdom of Manticore clearly the good guys going up against the bloated, expansionist People's Republic of Haven that has to expand to stave off economic collapse. The Havenites get even worse in some respects when a coup overthrows the government and the new leaders authorize policies that make the original regime seem downright benign in comparison (this is the series that named State Sec), but while that's going on, several Havenites were given rather deep characterization that showed that most of them were decent people who were rather powerless to improve things. At the same time, many Manties were introduced who were rather self-centered at the expense of others, if not downright evil; the same happened with most of Manticore's allies. Almost every faction, good and evil, has been deconstructed at some point to show that everywhere you go you'll find some bad people, some virtuous people, and mostly neutrals who are rather swayed by the people in charge. About the only groups still firmly at one end of the spectrum are the Masadans, or at least the men of power there, and those secretly in charge of the Mesan Alignment, both of which are decidedly evil.
- Galaxy of Fear has hints of this right at the start, where Hoole tells the protagonists that no, the Empire isn't a monolith of evil, but the early books still all have pretty black and white Imperial and Rebel representation. In the later books there are still loads of evil Imperials, and there's reluctance to really tarnish our heroes, but there's an Ineffectual Sympathetic Imperial and a cold but fair Noble Demon one. Some heroic characters are also forced into doing unheroic things, but a point is made that these don't come easily to them.
- Buffy the Vampire Slayer started with purely evil vampires but just one exception; over the seasons, the need for more interestingly human villains and the larger point about power the series builds to has grayer elements, like more humanly motivated vampires, and even relatively harmless but ostensibly "evil" demons. The Spin-Off show, Angel, went still further into gray with the premises and universe Buffy originated.
- Lost developed this in later seasons with the Others, whose motivations were pretty mysterious to begin with, but especially with Ben (the leader of the Others), who is pretty firmly established as a bad guy even though he constantly claims that he and his people are the "good guys" (and he's also a notorious liar). In later seasons, however, Ben becomes more sympathetic, due to both his Freudian Excuse and the fact that he's an interesting character. By the end of season five he's actually been ousted as the Magnificent Bastard because of the fact that he's been manipulated by someone who appears to be more evil than he is (Jacob's enemy). Maybe. Unless Jacob is the bad guy, because Jacob is leading the Others, and they're bad...unless they're not. And of course, the island is frequently visited by people who are definitely worse than the Others, and Jacob is the sworn enemy of a guy who despite not starting as such, is said to be Made of Evil.
- Once Upon a Time eventually gives Big Bads Rumplestitskin and Regina backstories that can give them a good argument for being The Woobie, and Snow White commits a calculated, cold-blooded murder (albeit, it was a great case of Pay Evil unto Evil).
- Power Rangers started out with wholesome community-minded teens vs evil petty space aliens. Around seasons six and seven it started having some villains that weren't wholly bad (Ecliptor, Astronema, Villamax) and some heroes that weren't completely good (the Magna Defender). The series has never completely stepped away from Black and White Morality, but there's some shading to it now.
- Power Rangers Time Force was a radical shift. After Ransik lectured the Red Ranger about his origins, the Ranger was really troubled. You can seriously ask whether the Rangers are protecting innocents from monsters, or they are the armed force of a dystopian society destroying anyone not perfect. Doesn't help that the Rangers cryogenized the mutant instead of killing them, which the fandom interpreted as Fate Worse Than Death instead of mercy.
- Terminator: The Sarah Connor Chronicles starts out with Skynet being clearly evil and the Connors being clearly good, but the Connors' efforts to stop Judgment Day quickly make them Not So Different from the robots they're fighting, to the point that they openly admit to being terrorists. Their Graying Morality is really driven home in "Dungeons and Dragons", when Sarah repeats Kyle Reese's warning about the Terminators from the first movie... but this time it applies to Derek murdering Andy Goode in cold blood.
- Each iteration of the Star Trek franchise seemed to get a bit "grayer" than the one before it; The Next Generation was grayer than the unabashedly utopian original series, Deep Space Nine was grayer than TNG, and by the 2009 film Kirk's originally heroic archetypal traits straddle the line between heroic strengths and serious personal faults.
- The John Finnemores Double Acts episode "Wysinnwyg" pulls this off within a single 28-minute radio play.
- Hitman: Blood Money has the first time 47 kills an innocent man, and he kills other innocent men later on, signaling a shift from the earlier games' morality.
- The original Mega Man series is fairly Black And White. The sequel series get less and less so.
- In the Metal Gear series, the first game is very straightforward: you are to stop the leader of Outer Heaven to prevent war. Even though the leader turns out to be your commanding officer, it's very clear that you're supposed to stop him anyway. As the series goes on, it becomes less and less clear who, if anyone, is actually evil and not just a Well-Intentioned Extremist.
- Word of God has it that this was intended to occur over the course of the first Geneforge game. Arguably, it's more subtly developed over the course of the series, as the rebels got more opportunities to make their arguments (and even took the spotlight in the fourth game.)
- Command & Conquer: Tiberian Dawn was very black and white, but by Command & Conquer 3: Tiberium Wars the two sides are very very grey
- Mass Effect was a very clear-cut black-and-white sort of game, but Mass Effect 2 descended into the realm of Black and Grey Morality. Mass Effect 3 was comprised largely of very, very grey decisions, and even tried to make the Eldritch Abominations a lighter shade of black.
- While many of the subplots of Dragon Age: Origins are very gray and many of the characters are morally questionable, the central conflict is between humanity and horrifying parasitic near-mindless monsters that love rape, cannibalism, and slaughter. The expansion pack Awakening features those same monsters, but some of them are not so mindless and evil, and one of them wants to stop his brethren from trying to destroy the world every few hundred years, albeit in a way that inadvertently caused the very invasion he was trying to stop. Dragon Age II takes it further; the central conflict is between factions of people who do bad things for good reasons, most of the major characters are deeply flawed, and no one person or entity is the Big Bad.
- BlazBlue already started with Black and Gray Morality, but most groups still get more nuanced as the story progresses. The mostly good Sector Seven gets more of its dirty laundry put out to air, revealing that Kokonoe keeps a loaded nuke silo as a "solution" for Terumi and aided Relius in making a core for Ignis, and the upper management redeploying Azrael; the defecting Makoto and Noel are only onboard due to picking the lesser of two evils. Meanwhile, NOL Main Branch gets Litchi Faye-Ling, and the Mutsuki house is unsatisfied with how NOL runs things and its leader Kagura Mutsuki is planning a coup.
- The opening scene of The Elder Scrolls V: Skyrim makes sure you hate The Empire - they're prepared to execute several carts full of prisoners, including at least one for a petty crime (and they proceed to chase him down and kill him when he tries to escape) and one (the Player Character) merely for crossing a border when they happened to pass by. As the game progresses, and especially if you join them, you come to realise that things aren't as simple as they seem on both sides of the civil war.
- Assassin's Creed III. Unlike the previous games, where the Templars were Ax-Crazy sociopaths and/or megalomaniacal tyrants with delusions of godhood, here most of the Templars Connor encounters are Well Intentioned Extremists who genuinely believe they are doing the right thing and that Templar rule truly is the best course for the world. We also start to see cracks in the Assassins' claim as the "good guys" when the Patriots basically stab Connor and his tribe in the back, and he is forced to fight them to avoid further conflict.
- Almost every game in the Tales Series does this, with the story starting out like a typical Black and White Morality Cliché Storm before eventually revealing the villains have understandable motives and occasionally the heroes may not be entirely good.
- Haze attempted to pull off this trope when the player defects from Mantel after realizing that the Promise Hand isn't as evil as he's been led to believe. Unfortunately, the developers botched it pretty badly-the Mantel troopers are Obviously Evil even when you're on their side while the Promise Hand faction is basically portrayed as saints.
- Spec Ops: The Line, a Continuity Reboot of the Spec Ops franchise, moved the series firmly into Grey and Gray Morality territory (or Evil Versus Evil, depending on your interpretation), as opposed to the comparatively idealistic earlier titles.
- Touhou was never blatant good vs evil - everyone, main characters included, have always been huge jerks at best, and "villains" were more prone to Poke the Poodle - but at least starts with clear protagonist and antagonist lines, with youkai causing trouble for selfish reasons and the humans going out to beat them up until they stop. Then Continuity Creep and Going Cosmic happen, delving deeply into the nature of the relationship between youkai and humans. This is most apparent in the Expanded Universe; Wild and Horned Hermit is mostly told from the perspective of youkai and greatly humanizes them (for lack of a better word), portraying them as well-meaning and friendly, but still with a nasty streak that could come out at any time. Forbidden Scrollery meanwhile is mostly told from human perspectives and portrays youkai as corruptive and malign influences that need to be kept separate from humans at all times (for the benefit of both groups), but all the most brutal and callous acts in the manga are performed by humans. And Symposium of Post-mysticism is a debate between the various powers jockeying to control Gensokyo, about the future of the region and the nature of human/youkai relationships, all having excellent points even if they're all ultimately acting from self-interest.
- It really depends on the ending route of Aviary Attorney how this goes; in 4B (Égalité) everything seems brighter and in 4C (Fraternité) circumstances make the heroic characters more heroic and the unheroic characters much worse. But in 4A (Liberté) Jayjay Falcon loses all his faith in justice and becomes a Vigilante Man. His assistant Sparrowson loses most of his Comic Relief characteristics, becomes more serious about justice, and can decide whether to let a known murderer go free or burn to death, as well as whether to turn in Falcon to be tried and executed.
- Carmilla the Series Season 1 has the completely good Ragtag Bunch of Misfits against the completely evil vampire coven, with one of the seemingly evil vampires being Good All Along. Meanwhile the apparent villain of Season 2 is not as evil as everyone assumes, the apparent helpful character is a Well-Intentioned Extremist, and the main characters make a lot of things worse and keep performing morally questionable actions just to stay ahead.