Graying Morality

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 Grey Morality or Grey and Grey 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.

Examples of Graying Morality include:

Film

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. In Return of the Jedi, Luke is told that he must kill his own father or the Emperor will win.

Obi-Wan: Luke, you're going to find that many of the truths we cling to depend greatly on our own point of view.

- And don't even get us started on the expanded universe.
- Or the prequels. Child Soldiers and slave army, anyone?
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.
- The films begin with Dr. No and From Russia with Love and both those movies are pretty gray, the latter revolving around Bond manipulating a woman into stealing a MacGuffin (albeit unaware she's a double agent). It gets somewhat less so with Goldfinger and the others, but really how gray a Bond film is really depends on the film itself, and is pretty cyclical. Casino Royale wasn't Gray because the series was light, but because the Brosnan films were (Licence to Kill before them being the darkest and most gritty Bond ever film.) Plus, Bond is Bond- a smoking, drinking, womanising state spy and assassin, and all that entails, in every appearance. He's a Jerk with a Heart of Gold at best.
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.

Literature

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 say 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 Dresden Files. So much. When Harry and Ebenezer are starting a conspiracy to counter the Black Council, Harry names it the Grey Council.
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.

Live Action TV

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.
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.

Music

Billy Joel's song "Shades of Grey" is about this phenomenon occurring in his Real Life.

Multiple Media

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.

Web Originals

Effectively the entire premise of Phantasia.

Video Games

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.)
The Original Command & Conquer was very black and white, but by C&C 3 the two sides are very very grey
Mass Effect was a very clear-cut black-and-white sort of game, but Mass Effect 2 has descended into the realm of Black and Grey Morality.

Western Animation

So far, The Legend of Korra compared to Avatar: The Last Airbender.