AD Police, the spin-off of Bubblegum Crisis, is darker, more violent and adds some psychological spins to the original series concept. The TV spin-off they produced to this spin-off a decade later surprisingly was closer in tone to the original Bubblegum Crisis.
Little known fact: AKIRA was conceived as a Darker and Edgier retelling of Gigantor.
Osamu Tezuka's Black Jack is a rather dark series to begin with, save for some comedic touches usually provided by Pinoko. Osamu Dezaki's video adaptation in the 90's however takes the darkness to new heights and becomes a high-tension, highly stylized tragedy.
Bleach already had a fair amount of blood and guts by the standards of Shounen Jump, such as a silhouetted photograph of Souken Ishida's mutilated, tortured corpse, and a young child being used by a serial killer to murder innocents. However, the Thousand Year Blood War has cranked the gore and violence up a notch. Key good guys are finally killed off, usually with gaping holes where part of their body used to be; at least one captain is shredded so completely that his chest is ripped open right to the very visible spine and rib cage. Adhering to the classical Shounen battle conventions gets protagonists killed, and the Big Bad commits multiple genocides - not only against his enemies, but against his own people, too.
Choujin Sensen: Compared to the author's previous series like Gamble Fish, this definitely takes the cake in terms of graphic content.
Cutey Honey has had multiple reimaginings over the years, but among the darker versions was New Cutey Honey, taking the originally rather silly premise of Cutey Honey with its sometimes squicky humor and transported it Twenty Minutes into the Future, making things much darker and upping the Cyberpunk elements.
The Movie installments of Doraemon can easily feels like this, even if Nobita and friends remain good people. One movie deal with the horrid effect Black Magic (in a magical world), which comes from devils (who are aliens). Another deal with the revenge of the Reptilian people evolved from dinosaurs, who want to alter time so humans never exist. Yet another deal with the horrors of war as terrifying aliens (who are humans in hazmat suit) invade a utopian planet inhabited by cute humanoid animals. The last one has a particular scene that can't be anything else but traumatic to its supposed audience.
The Big Bad is The Man Behind the Man to Ultear, who has been The Chessmaster to several other big bads. Not only that, but he's the first one in the entire series to ever beat Makarov in a fair fight. Makarov's only other loss was due to a sneak attack.
Most, if not all, of Hades' Quirky Mini Boss Squad are more powerful than previous Big Bads. They use lost magic, which is absurdly powerful. One of them is basically a more powerful version of Natsu. He can eat Natsu's flames, and uses fire that Natsu chokes on.
And to top it off, the goal of the whole thing is to revive the Black Wizard Zeref.
And all of the above is nothing compared to the Tartaros arc. While most of the previous arcs' conflicts' scope was limited between Fairy Tail and dark guilds, the Tartaros arc has now involved innocent civilians with well over a hundred deaths and counting.
And the Arc starting with Chapter 439 might dwarves all of the above combined, time will tell.
Fate/Zero is a Darker and Edgier prequel to Fate/stay night — intentionally so, since the novel's intent is to show just how dark, depressing, and violent the Holy Grail War can be. This was to be expected, because the parts of the backstory already revealed Fate Stay Night make all but a tiny handful of the Fate Zero characters Doomed by Canon.
The FLCL manga is much darker and more bizarre than the anime its rather loosely based on. An example of this would be Naota killing his dad with a baseball bat.
Front Mission is known for being a war drama, but Dog Life and Dog Style takes it Up to Eleven as it incorporates the grittiness of Red Eyes in a completely uncensored and brutal manner (Which relates the journalist who brings out the uncensored truth). In the first two issues of the manga it starts off showing gruesome death, rape/sex and ultra violence.
The first anime of Fullmetal Alchemist was, in addition to being 50% Gecko Ending, notably more pessimistic, morally grey and low-key than the manga and Brotherhood. Most of the characters' stories ended notably darker, the Quirky Miniboss Squad had a much darker origin as failed and abandoned human transmutations performed by several different alchemists, and instead of impressive alchemical fight scenes like in Brotherhood most battles were brutal, short, and often weighed towards the villains.
If one thought that Yuu Watase's Fushigi Yuugi Genbu Kaiden was merely Fushigi Yuugi from two hundred years ago... uh, nope. Not only the heroine Takiko comes from a very different time in the real world (more exactly, Imperial Japan during The Roaring Twenties, in contrast to Miaka and Yui who come from the Japan of The '90s), but the Shi Jin Ten Chi Sho that she roams through is far bloodier and more complicated than the one we viewed during Miaka and Yui's journeys.
Gao Gai Gar FINAL is much darker than the television show for two main reasons: first, it's an OVA so they could get away with things that wouldn't fly on broadcast television, like explicitly sexual Fanservice. And secondly, it was aimed at a seinen audience rather than at children.
FINAL is an example of why Darker and Edgier does not necessarily equate with Dark and Edgy. The original show was far down the Idealism side of the sliding scale; the OAVs were just somewhat less so in comparison, and are still pretty darn light and fluffy, especially in comparison to certain other super robot shows.
Gigantor: The Tetsujin remakes also have a touch of this. While the 1980s version wasn't particularly dark, the look of the series was redesigned to make it less cartoony and whimsical and more like the modern, high-tech Super Robot shows of the day. This ultimately resulted in a little memorable show and when a sequel series, Tetsujin 28-FX came out in the 90s, despite the new robots being even more complex, overbuilt and gimmicky, with transformation and combination gimmicks and such, the original Tetsujin was drawn in the classic style, googly eyes and all. The second remake in the 00s, from the people who brought you Giant Robo, took it in a whole new direction, keeping the cartoonish 1950s visual style and wrapping it around a grim story about war and political intrigue... and a boy detective with a giant cartoony robot.
Higurashi: When They Cry utilizes this about every 5 or 6 episodes. Each arc begins with a few gruesome shots of one of the character's deaths, and then proceeds to be lighter and happier for a while, while steadily approaching the doom shown at the beginning of the arc, getting darker as it goes on.
Umineko: When They Cry not only follows a similar formula, but also has this trope by actually BEING darker and edgier than Higurashi. At least Higurashi was limited to depicting things that are relatively down to earth. Umineko gives us witches who do whatever they want, often to brutally graphic extents. One even delights in killing her victims in brutally creative ways, only to revive them and do it all over again. And when they're done with the killing they'll start with Mind Rape that makes Higurashi look like Casey And Friends.
In regards to anime adaptations, the 1999 TV anime has a much more somber and moody tone than either the original manga or 2011 remake. It also amplifies the focus on Killua's moodiness and Kurapika's PTSD.
The whole manga really, when compare to most Shonen mangas. Each arc is filled with it's fair share of gore.
It's also a deconstruction of Shōnen manga and anime.
The series was dark before, but in the York New arc, it's the first time it goes into truly grim territory.
THE iDOLM@STER - while the first half of the series was very lighthearted, the second half progressively began to take on darker tones, culminating in 765 Pro's rivalry with 961, Chihaya's dead little brother plot, and the Producer getting into a life threatening accident.
For a show about fluffy animals who are Inept Mages, Jewelpet likes to pile on the darkness in some seasons:
The second season has one of the most cripplingly shy leads in anime; she does not immediately become healed of her shyness by meeting Ruby, which was done with Rinko in the previous season, and her insecurities nearly cost her her powers one time. Additionally, the villain is a girl passing for a boy, who is the Separated at Birth twin sister of the boy Akari likes and wants to take down God as revenge for leaving her mother in a coma as she sacrificed herself to stop Dark Magic from flooding the world. Few Jewelpet villains have been as tragic and conflicted as this one. Oh yeah, and she kills one of her own Jewelpets. Onscreen. (But she gets better. Like 26 episodes later.)
The third season does a good job of faking you out at first with its Gag Series nature. Then the Love Triangle kicks in. And holyshit, isitacomplexone. And then there's the final arc, featuring God becoming corrupted by Dark Magic and mass-killing everyone she fails to convert to darkness (but they get better), except for seven people who turn out to be The Chosen Ones.
Jojos Bizarre Adventure began as a shounen manga, but eventually switched to a seinen magazine early on during the 7th part, Steel Ball Run. Steel Ball Run is the darkest part of the entire franchise with the most self-centered, cynical main character in the entire series' history, and a more psychological and character-driven storyline with more adult themes such as sexual assault, domestic abuse, and homosexuality. The 8th part, Jojolion, hasn't quite been as dark but still has many of the same adult themes as SBR.
Karakuridouji Ultimo seems to follow a zig-zag pattern with this trope and Lighter and Softer. The series started fairly light hearted, and comical, up until the chapter where Ultimo, the embodiment of good, beats up an evil doji into a rather nighmarish pulp while smiling. Then they threw in the main character's best friend turning into a Yandere, the world blowing up, and the entire good cast being killed quite brutally. Once everyone got better in Part 2 of the series, it went back to its original state, but then implied to have killed off most of the original Good Doji Masters. Then Part 3 got even worse, by having the earlier mentioned Yandere nearly rape the main character in a rather dark manner.
The 1980's remake of Kimba the White Lion by Osamu Tezuka. The final episode has about a good chunk of the cast die.
Lupin III, which we include because a fan is more likely to be familiar with the anime equivalents, rather than any of the comics that came first. It establishes itself as a series with sex, violent death, and occasional Gorn.
The Woman Called Fujiko Mine brings back many of the darker elements from the manga back to the screen. The sexual nature of Fujiko, Mind Rape, and violent deaths are played up in this series.
The annual specials can spend some of the time Darker, and some of the time Lighter.
Dead or Alive is the darkest of the Lupin Theatrical Releases, and has the notable honor of Monkey Punch working on it.
The OVA of Magical Play is a much darker affair than the slapstick comedy of most of the original series—up to and including characters dying horrible deaths in big puddles of blood.
Magi – Labyrinth of Magic: Oh boy. The manga started with a light hearted, optimistic plot, and despite a bit of drama, it was quite happy. But then arrived The Magnostadt Arc. And everything after it, to be honest. Alma Torran takes the cake, by showing just how much crueler this manga came to be. David's slaugher, Tess' death and Aladdin's parents, the soldiers Hakuryuu is manipulating...the list goes on. To this, you can add Hakuryuu's Face–Heel Turn, and the manga's themes became darker, or at least more serious than they used to be. At the moment, there are more manipulation, murder, and mayhem than one would have expected when reading the summary. And it seems it's only going to get worse.
Meg not only lost fights, but she had to face serious consequences (deaths, injuries, humiliations, etc.) that could 'not be undone with magic.
Martian Successor Nadesico has Prince of Darkness as its Darker and Edgier Title, the plot becomes a moodier and much darker plot of the original series as many a dream is destroyed and it was not well received by fans at all
Mawaru-Penguindrum starts off like a comedy where three siblings have to deal with invisible penguins and get a girl's diary, but Ringo eventually tries to rape Tabuki, Kanba becomes a terrorist to save Himari, Yuri tries to rape Ringo, Shouma can't cope with how his and Kanba's parents seemingly caused the death of Ringo's sister, etc.. At least she changed her mind.
Mazinger Z, Trope Codifier of the Super Robot Genre was considerably darker than former Humongous Mecha shows. The Professor was actually a Mad Scientist. The Hero was a JerkassIdiot Hero teenager -as opposed to the good-natured child that starred Gigantor- that destroyed half city accidentally the first time that activated his robot, nearly got killed in his second fight because his mecha's cockpit offered very little protection (he started to wear a protective suit and helmet to prevent that). His enemies often attacked him when he was away of his robot, and in a storyline they invaded a village and started to kill all people that they deemed useless in a way Nazi-like manner.
Great Mazinger: Its sequel was darker. The show dealt with themes such like racism and parental abandonment, the main character was a Deconstruction of the archetype that Kouji introduced, the Tsundere had mood shifts due to mental issues that had little to do with Tetsuya, The Professor was a very questionable father figure and mentor...
Gundam SEED, to frankly put, is extremely dark for an Alternate UniverseGundam series. There are brutal atrocities committed by both sides which becomes a Guilt-Free Extermination War with very little in the way of clear comic relief. There is no mercy, no honor, no salvation for anyone. Civilians and soldiers are equally expendable, and not even one's own allies can be trusted. Victory for either side means virtual destruction of an entire subtype of the human race and by the end, all of it.
Oh, and the explicit horror isn't where it ends. You know all that genetic manipulation that forms the backbone of the series? Yea, turns out that the entire thing was taken to the logical extreme by essentially using live humans and clones as disposable test subjects. Not only did this fail to produce an implementable solution to the coordinator issue, it spawned a living representation of all of mankind's sins against itself, the last clone Rau Le Creuset, who is determined to enact a sick, yet horrifyingly justified restitution upon the human race.
Gundam 00 took this closer to home by placing the series in the Anno Domoni timeline where most of the world's current problems aren't just still around, they're exacerbated, and it's going to take a lot of blood to get any work done on them at all. This also makes it one of the darkest alternate universe Gundam, up next to SEED.
Until the movie suddenly snapped everything into hope and rainbows, giving us one of the few unequivocally happy endings in Gundam. It even has world peace.
Gundam AGE unveiled its true colors from episode 14 onwards. Similar to Madoka, don't let the series' kiddy art designs fool you. While initially masquerading as a children's Gundam series for the first 13 episodes, the Love Interest gets brutally killed in episode 14 and The Hero consequentially takes the dark descent into becoming a genocidal Knight TemplarWho Fights Monsters. Oh, and the UE are Human All Along. And those hoping for a bloodless final episode was hopelessly crushed at it ends up in a Tomino Kill'em all for BOTH sides. Add the almost-complete absence of comic relief and the series being set in a Crapsack World that would feel right at home in the Universal Century or Cosmic Era, and you got a series that somehow manages to get up there with SEED and first part of 00 as the darkest AU series yet.
Where the Gundam series is concerned, it's sometimes darker and edgier in their side stories, regardless of the calendar. Comic relief aside, the overall progression of arcs, foreknowledge, the ending and themes show that the likes of Mobile Suit Gundam 0080: War in the Pocket and C.E. 73 Stargazer to be less sunshiny than their respective calendars' main series.
To a point Gundam franchise in general was darker and edgier in comparison to the other mecha anime around, with the themes, the (generally) Grey and Gray Morality, the various War tropes present and the franchise was started by a man known as "Kill 'em All".
Naruto Shippuden/Part II has been increasingly darker than the original series. The main character, Naruto, loses the closest thing he has to a father, Jiraiya, his village is nuked, his mother figure Tsunade is knocked into a coma, he is put into a Breaking Speech by Pain which he couldn't retort to... even though he managed to get Pain to bring everyone back to life that he killed that day, the Village is still a crater, Tsunade is still in a coma, and Danzo nearly became Hokage. THEN we get to Sasuke, his former rival and best friend who had joined Akatsuki and attacked Killer Bee, and then attacked the Kage Summit. Learning how far his best friend had fallen caused him to have a Heroic BSOD and fall into an Angst Coma. Shippuden/II has more death, destruction, horrors, and Orochimaru-and later Obito creepiness to show it's much darker and edgier than Part I.
The Noozles took a grimdark turn about halfway though, with the introduction of Koalawallaland, its human-hating Nazi Koala inhabitants, and the threat of a Reality-Breaking Paradox due to the separation of the two universes being accelerated by seismic testing.
In One Piece, the 6th movie, Baron Omatsuri and the Secret Island, the Straw Hats start to separate from each other, due to conflicts the antagonist is creating. The plot also contains some of the biggest horrors, as Luffy's comrades are eaten by a Man-Eating Plant called "Lily", the Big Bad's backstory is also different, showing that his crew died, and he found Lily, allowing him to create Replacement Goldfish, so long as he feeds Lily, the movie's plot is also slightly more complex.
In the series proper, we had the Water 7 arc, easily the darkest arc in the series the Merry Go is deemed unfixable and can't sail any further, Usopp leaves the crew when the news is broken to him leading to a fight with Luffy, Robin disappears and later aids in framing the Straw Hats (though not without good reason) and the crew is nearly killed upon meeting the CP9. Oh and of course Robin's flashback the followig arc. Likewise the last bits of the first half have been leaning toward this the such as Ace finally finding Blackbeard and losing the introduction of World Nobles, the crew getting beaten by a Admiral and getting separated from each other. Luffy finding out about Ace's execution and breaking into Impel Down to rescue him, not only failing but nearly dying in the process. Then of course the whole war that followed to rescue Ace that ultimately ended with Ace dying, Whitebeard, one of the most powerful Big Good pirates on the planet being killed by Blackbeard and having his earthquake power stolen. Luffy actually doubting his dreams and a flashback that showed the (supposed) death of a close friend of theirs. Granted Luffy recovers and the crew reunite but even then dark times are on the horizon as Akainu, the Admiral who killed Ace, is now head of the marines. So...yeah.
In-universe example in Ouran High School Host Club: Renge's first appearance has her making a video where the normally-cheery members of the club become darker personae, e.g. the Keet becoming a callous bully.
Urasawa's Pluto does this to Tezuka's Astro Boy, showing the grittier side of life in the twenty-first century. This being Urasawa, it works tremendously well as the writing and themes are thoughtful and touching as well as dark and edgy.
Pokémon Special, a manga spinoff of Pokémon's video game series, has fights to the death for everyone, humans included.
Pokémon: Diamond and Pearl Adventure! is this in a way. Not in terms of violence, though it has been described as "Dragon Ball meets Pokémon" and is hefty on the fighting, but more-so in the plot. Especially when Mitsumi and her past is involved.
As far as the Pokémon anime goes, Diamond/Pearl and Best Wishes are both noticeably darker and more serious at times than much of what came before it, some even surpassing the games, though the original Kanto season had its fair share of dark moments as well. Still, it is generally lighthearted and makes it clear that it is aimed at a young demographic.
Pokémon Origins has 4 episodes, but shows it's definitely darker. The fighting is more brutal involving worse attacks, blood-curdling screaming from getting bitten and almost dying, or being beaten to death by a stun baton, and a Mewtwo that is portrayed as a powerful psychotic monster.
The movies in general are this, most of them having at least one of these features:
A subject that's more serious or complex than usually found in the TV series.
The very first episode was this when compared with the vast majority of subsequent episodes, what with Ash being chased by a flock of murderous Spearows and the implications of being a 10-year-old traveling out into the world on one's own. It was written by Takeshi Shudo, the original series director from Kanto until Johto, and if looked at closely, the trope applies to most episodes written by him, though not as overtly.
Zigzagged in the Pretty Cure franchise. Some installments are dark, but most are light. The dark ones usually have one or more of the eponymous magical girl having to deal with personal failure that cost them dearly. The reigning champion of Grimdarkness is currently Heart Catch Pretty Cure, with Cure Moonlight having to deal with her Fairy Companion dying in front of her, her father being The Dragon, her father killed by the actual Big Bad in front of her, her Evil Counterpart is actually kinda-sorta her little sister, said little sister dies in front of her by her own hands, and then figuring out that even saving the world won't bring them back. Hurting Hero, she is.
DokiDoki! Precure seems intent on One Upping the above, by not only having an expy of Yuri, but by also showing, onscreen, an entire kingdom being devastated by the Big Bad (Previous seasons merely gave a small glimpse of how the big bad operated and the devastation in his wake), as well as being the only series in the franchise to date to subvert one of the then standard formula practices in the series, in that a Dark Magical Girl, when redeemed, automatically stays on the side of good as a Precure in Regina, only for her to almost immediately be forced back onto the side of evil by the Big Bad, who's one of the most evil Big Bads since Gooyan... and he's not even the Big Bad that appears for most of the series and is in fact controlling him. Damn.
Every adaptation of Read or Die seems to do this. The manga is fairly light-hearted (and the Read or Dream manga entirely so). The OVA has a bit of camp to it, but gets fairly dark, with a Bittersweet Ending. The TV series, R.O.D the TV, manages to get more depressing nearly every episode, but eventually rewards its long-suffering cast with a happy ending. Strangely, they keep improving.
Magical Record Lyrical Nanoha Force is said to be Darker and Edgier by the writer. And he wasn't kidding. In the 3rd Chapter, we were introduced to Card-Carrying Villain Veyron who introduces himself by killing everyone in a chapel that Touma had visited earlier. We won't see Nanoha fall to the dark side but definitely we will see more people being offed by Belkan weaponry then usual and maybe a few kills with Mid-childan weapons. Then, a few chapters later, there's a brutal fight between Lady of War Signum and the Dark Action Girl Cypha, which involves the latter being partly dismembered and the former, landing in a pool of her own blood with a sword in her gut.
And how Touma's device is relies on The Corruption to work, and Lily is a source of death and ruin as she accidentally causes people to degrade to Body Horror like meat blobs
Two notable instances in the first season. Nephrite's death and (outside of the first few minutes) the entire two-part finale, where Makoto, Ami, Minako and Rei are all killed one by one, then Mamoru, and finally Usagi after disintegrating Metallia/Beryl with the power of the Silver Crystal. Luckily, they get better, but it was still a sudden horrible two episodes for a mostly lighthearted show up to that point.
The S Season, which is overall darker than its predecessor. While overall pretty light-hearted, featuring some progressively sillier monsters (as well as Eugeal's car appearing in progressively sillier locations.), once Mimete's removed from the picture, the season takes a dark turn. You know a season's about to get real when the final group of villains don't even bother to summon the silly monsters of the week their predecessors summoned.
The villain Queen Nehelenia appeared in two seasons, and the contrast between which is huge. Season 4 was mostly rather light-hearted: there was a pegasus, the villains were campy circus people who were commanded around by a weird old lady, and it focused mostly on Chibiusa; only at the very end there was a real difference. The first part of season 5, however, was entirely different, even breaking with the usual format. There were no monsters of the week, only Nehelenia's nearly indestructible mirror minions. In the course of the arc, Mamoru was brain-washed once again, resulting in Chibiusa almost fading, and all the Inner senshi were taken out one by one, sometimes in very painful manners (like Makoto being electrified almost to death by Nehelenia herself). This arc also brought back the outer senshi, who have a much more cynical approach to these matters... and they also get taken out. Usagi barely manages to win, but before that she has to go through a full-blown Break the Cutie process that almost throws her to the Despair Event Horizon. (And how does she win? Via offering herself to be tortured and killed by Nehelenia, who also shows heartbreaking Hidden Depths as we learn about the process that made her... well, the way she was. Only then things start going back to Lighter and Softer.)
Even more so, the last part of Stars. Where after a long search, the Sailor Starlights are reunited with their Princess... only for her to be killed. Then the Inner Senshi get killed. And we find out Mamoru has beenDead All Along for a while already. AND Haruka an Michiru kill Setsuna and Hotaru as a part of a Fake Defector plan, but fail and die at Galaxia's hands. And we're not done...
If you only know Yoshitomi Akihito for his kawaii Yuri short stories, then School Mermaid, a horror manga, will take you by surprise.
Once in The '70s, there was a short shonen manga by Kazumasa Hirai and Hisashi Sakaguchi. Its name was Wolf Guy, and it was about the adventures of young werewolf Akira Inugami and his Hot Teacher Akiko Aoshika. Decades later, Yoshiaki Tabata and Yugo Yuuki (the authors of Akumetsu) took the basic concept of this manga and re-made it into a seinen story named Wolf Guy - Wolfen Crest - which is full of Gorn, Fan Disservice, etc. Inugami gets almost killed several times, Aoshika-sensei is almost completely broken in all senses, and Big Bad Haguro Dou goes from a mere Yakuza heir to one of the most despicable villains in manga.
The World God Only Knows, A light-hearted manga-series about a Otaku playing video-games and using that video-game knowledge to help women in real-life get over their problems which in the process leads to the creation of an Unwanted Harem. Read the early chapters that highlights the before description, and then skip directly to chapter 214. You'll be amazed at how dark the manga becomes. To elaborate, what starts off as a comedy/romance manga series, slowly begins to showcase Shounen-style action during the later portion of the Goddess arc, and then delves further to even showcasing blood-and-gore once it reaches the Past arc.
Yatterman Night serves as one for the original series. For starters: Dokurobei manages to destroy all of Dekkaido in the first few minutes of the show alone. The Doronbo have been exiled, and their descendants have to deal with the repercussions. The Yattermen turn what's left of Dekkaido into a walled kingdom with thousands of robotic copies on guard, and their descendants live in the poverty-stricken outskirts of said kingdom after having their parents worked to death. What used to be a silly show about a couple of preteen toymakers fighting crime has turned into a rather serious drama.
The Yu-Gi-Oh! manga when compared to its two animeadaptations, which tone certain things down, including the atmosphere. Most of Dark Yugi's Penalty Games in Toei's anime are turned into illusions, while they are turned into Mind Crushes in the Duel Monsters anime. More characters are also Killed Off for Real in the manga. Particularly, Pegasus and Bandit Keith (if you don't count R as canon).
Even more so when compared to the second anime's English dub.
Ryuji Otogi's background story is completely different than in the anime, which no longer involves butthurt and Pegasus, but involves domestic abuse and a father who aged rapidly due to losing a rather satanic Shadow Game with Yugi's grandpa.
In the Toei anime, as previously stated, much of the death-related Penalty Games being turned into illusions, but then there were also chapters being either skipped or altered because the content in them was too violent/disturbing (the knife game with Ushio was changed to a game of drawing playing cards). The most notable altered storyline being Death-T, which replaces the chainsaw-wielding Chopman with the more kid-friendly "Game Masters." Kaiba's butler dying from electrocution is also removed. The Duelist Kingdom arc was treated similarly in the second series anime.
The manga is definitely darker compared to the succeeding spin-offs of the Duel Monsters anime.
On the flip side, Yu-Gi-Oh! 5D's went the way of AKIRA in order to achieve Darker And Edgier. In fact, popular consensus among the show's fans is that the sheer spike in Darker And Edgier material in it was a deliberate act to keep 4Kids Entertainment from Macekreing it... not like it hasn't stopped them from trying.
Speaking of Yu-Gi-Oh!, Yu-Gi-Oh! GX went from the brainwashing cult of season 2 to the way darker tone of season 3. It started out with new main characters as usual and a seemingly tame (at least compared to season 2) villain until he gets defeated relatively quickly and then the series gets much darker including the characters dying when they lose a duel, at least that's what they are told, the main character getting tricked into releasing his Superpowered Evil Side and killing some of his remaining friends, and the The Man Behind the Man/Stalker with a crush/Hidden Agenda Villain possessing the main character's best friend. Although 4Kids Entertainment ruined season 3's dark tone in the dub, watching the Japanese version makes the dark tone obvious.
And staying with GX, its manga version is much darker and serious than the anime. Several characters turn out to be possessed by the Big Bad, who is a truly depraved monster with a connection to the creation of the Millennium Items.
Yu Gi Oh Zexal appears at first glance to be Lighter and Softer after 5D's, but then it turns out that Dr. Faker and Mr. Heartland have been running highly dangerous and illegal experiments on children, including Faker's own sons. Kite resorts to murder in an attempt to save his brother, only to learn the whole thing was a lie, and he comes to despair of his own salvation. Astral, Yuma's spirit companion, was in fact sent by his people to commit genocide. Rio was severely burned in a dueling accident. Shark and Rio are actually dead and are Barian Emperors. Then, the Barians initiate an Assimilation Plot to destroy the Earth and turn humans into Barians.