Many series with Black and White Morality end up gradually getting more and more shades of grey as they continue on. What looks like a simple conflict between good and evil in the early installments gradually becomes more complex, and in the later installments there are many more gradations of morality. More often than not, the process is an unintentional side effect of exhausting the story possibilities of simple moral conflicts and adding less absolutely good or evil characters for variety's sake. In other cases, it's a deliberate statement by the creators about morality and conflict in general.
This can happen to entire genres: spy stories, war movies, westerns, superhero comics and so forth all incorporate significantly more Black and Gray Morality or Grey and Gray Morality the longer the genres themselves are around. Also sometimes done intentionally as a means of averting or addressing Values Dissonance in especially long-lived genres or works; the Western, for example, has changed as our historical perceptions of the American frontier have grown more morally ambivalent.
Compare Cerebus Syndrome, Darker and Edgier and Grimmification, which can all sometimes involve this. However, plenty of works go through those tropes without shifting their basic moral scale.
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It's getting more 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. It's justified by the fact that eventually the Kishin could wipe out the whole world, but the situation at just halfway through the story is that dire. Believe it or not, it's gotten worse.
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 has undergone this as more series have been 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 has become more developed, the Federation has been 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.
Obi-Wan: Luke, you're going to find that many of the truths we cling to depend greatly on our own point of view.
The prequels are much greyer than the originals, Child Soldiers and slave army, anyone?
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.
The longer the James Bond film series has gone on, the more and more gray has crept in regarding Bond's role. (This was a feature in the original novels to some extent, but the films tended to ignore it.) The recent Continuity Reboot with Casino Royale seems to have started from the gray area.
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.
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 it with purely evil vampires but just one exception; over the seasons, the need for more interestingly human villains and the larger point about power toward which Joss Whedon was building gave us 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 (written by some of the same writers as LOST) is also headed here. When BigBads Rumplestitskin and Regina are given 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) you've landed here.
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.
This is a common theme throughout The Sarah Connor Chronicles. It 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 were seen as straddling the line between heroic strengths and serious personal faults.
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.)
The Original Command & Conquer was very black and white, but by C&C 3 the two sides are very very grey
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.
While more Black And Gray than Black And White, BlazBlue shows signs of Sector Seven turning darker and darker as more of its dirty laundry is put out to air. Acts of terrorism are the norm in works like this, but we soon learn that Kokonoe keeps a loaded nuke siloas a "solution" for Terumi, she aided Relius in making a core for Ignisand lost several of her workmates and nearly Tager over it, the upper management recently redeployed Azrael (someone who spent the whole time in prison because of uncontrollable violent urges to attack everything in sight, even allies) to the front lines, and said upper management and possibly Kokonoe left Bullet and her squadron for dead. It seems the latest recruits (Makoto and Noel) are only onboard due to picking the lesser of two evils - aside from whatever remnants are in Ikaruga alongside NOL Ibukido, their only alternative for supporting their families is NOL Main Branch, and both Terumi and Relius find the two girls... troublesome, to say the least. The feeling is mutual - continued murderous hostility from Captain Hazama (aka Terumi) and Noel's tempering into Mu-12 pretty much convinced them both that they've had enough of the Main Branch.
While the Main Branch is probably beyond help thanks to Terumi and Relius, NOL overall would probably get a little lighter thanks to having Litchi Faye-Ling since CS End, even if she's actually Forced Into Evil. Why? She still retained her kind aura and hasn't fallen into complete obedience for the sake of her desire to save Arakune as well as still not trusting the two monsters above, if she could survive and things are lucky enough, her influence might make NOL loosen up in terms of dictatorship. Tsubaki Yayoi, if she still has her lucid moments, still would try her best to serve the people, but since she's currently Brainwashed... Regardless, these also kept the NOL side from falling to even worse.
Adding further, there's also the fact that one family in the Duodecim, the Mutsuki house, the most powerful one at that, is unsatisfied with how NOL runs things and its leader Kagura Mutsuki is heard about planning a coup. For good or for bad, it's unknown so far, thus it mucked things up further. note If Kagura really thinks that the one making NOL fall even worse is really Terumi and Relius and trying to fix things, then probably the NOL side gets lighter, but if Kagura did it out of self-glory and thinking that he/she can rule the NOL better himself/herself in a selfish fashion, then the NOL side gets darker. Sure enough, Kagura ends up being announced as a console-exclusive character and he seems okay with storing Noel and Makoto, currently public criminals of NOL and talking with them more casually to further his coup plans.
Almost every game in the Tales Series does this, with the story starting out like a typical Black and White MoralityCliché Storm before eventually revealing the villains have understandable motives and occasionally the heroes may not be entirely good.