Brain Dead 13 is a game where the protagonist gets to die in all sorts of graphically violent ways, which has made it extremely hard to understand why this was given a K-A rating note (Kids to Adults, the mid-90's equivalent to the Everyone rating) then.
There's the whole issue with Vivi the vampiress and her titillating appearance, figures and Male Gaze, and one suggestive magazine in the Freeze-Frame Bonus that can be too suggestive for children, yet we may never understand why all of these are totally safe for kids with a K-A rating. What's even stranger is that Japan's game rating organization (pre-CERO) slapped each box of the game (exported from America) with an "all ages" (全年齢, zen nenrei) rating on a green sticker, hoping that its audience of children would be less sensitive to mind-numbing bloodless violence and sexuality than America's children (due to cultural differences). The proof is in the pudding here◊.
The iOS port averts this by ramping up the rating to a 12+, which is an equivalent of either a "Teen" or an "Everyone 10+" rating.
Dawn Of The Dragons is a Flash browser game that's marketed to children on kid-friendly sites like Kongregate with the promise of high fantasy and relatively simplistic gameplay. The premise is simple enough - a farmhand rises to become a champion. How that champion gets there, though, is brutal and unapologetic:
Text and images show enemies being dispatched in a number of gruesome ways (having their throats slit, being impaled by multiple swords, being decapitated, main characters being covered in gore and viscera). Several of these deaths are described with paragraphs going into detail about the minutiae involved, and how the main characters stand back to watch someone they've just sliced open bleed to death.
In "Peril of the Pumpkin Patch", two children are spied on and chased by creature with a flaming jack-o'-lantern for a head. His victim, the girl, has her head mounted on a pike (that is also seen in one of the chapter images), which is subsequently used to terrorize the residents of a local town.
The first game has a rather dark plot, and some references to the Bible. It also has some rather imposing bosses such as the Angler King. And when the boss Frostwind literally turns red, it looks like he's spitting blood when he opens his mouth. And it still got away with an E rating!
The DS sequel has the infamous ending, a woman nearly committing suicide so her son could be Mayor, and the main villain's reasons behind his scheme to seemingly end the world.
Kirby's Dream Land 3 has the infamous boss fight against the True Final Boss, Zero, a giant eye with a red iris who freaking shoots blood at you as an attack, and later rips its own iris out of its body in a gory manner to keep fighting and then explodes, shooting blood everywhere! That boss fight is whyKirby is reputed as Surprise Creepy.
It's practically a Running Gag for the Kirby series that it will feature pretty dark elements and Surprise Creepy moments with the latest game, Kirby: Planet Robobot, probably being one of the darkest in the entire franchise, only to still be rated E for Everyone!
The Legend of Zelda: Ocarina of Time has a dungeon and a sub-dungeon that include zombies, mummies, hands sticking up out of acid, walls made of skulls, really long arms that grab you, frightening music, and a creepy miniboss. In addition, Castle Town while Link is an adult is a ghost town infested with zombies.
The Legend of Zelda: The Wind Waker definitely looks like it's for kids, and had an E for Everyone rating to match. Then you start playing and the first thing you see is an intro screen describing that Hyrule and its inhabitants were destroyed biblical style, then you get to see the Re-Deads, then there's the climax where Link impales Ganondorf through the head and he turns to stone. Given these elements, saying this game is "kiddie" is a seriousFandom Berserk Button.
The trope began to be averted with later The Legend of Zelda games, which got higher ESRB ratings so they would be aimed at older audiences. Twilight Princess was rated T, and nearly every game from Spirit Tracks onwards, including remakes of previously E-rated entries, were given E10+.
Magical Starsign starts as a cute, fluffy game but once the second act starts things swiftly go downhill. There's too much horrible stuff going on here to list it all without taking up pages, but to sum it up: The main plot is about bringing mages to a planet where just being there turns them into into gummy-like inanimate blobs to be used as fuel for a space worm.
Mega Man X4 was when the Mega Man X series started to get dark. In Zero's opening cutscene, Zero is having a Nightmare in which there is blood on his hands. And don't get us started on Double. Mega Man X4 has an E rating.
Mega Man Zero looks like an average kid's game, but is the darkest series in the franchise, with the main plot being hinged upon genocide. And somehow the ESRB saw fit to give this game an E rating. From the bloody intro of Mega Man Zero to Elpizo'sear-grating scream, it's baffling on why it's rated E. And then there's Omega and Dr. Weil.
Super Metroid is a creepy, dark and atmospheric game that features one boss being stripped to the bone, and it got a K-A rating. Then when it came to Virtual Console in 2007, it still kept its Everyone rating. When it came to New 3DS Virtual Console in 2016, it was re-rated to a more appropriate Everyone 10+.
Metroid: Fusion. You begin with the story being that Samus was nearly killed by a parasite called the X, and you're dropped right into the BSL Research Station, which is, as far as you know, completely devoid of human life thanks to the X. Early on you have to navigate a series of eerie unlit corridors because there's been an explosion in the quarantine room. Turns out it's just a Hornoad-X, but if you explore a bit you find a room completely frozen. If you decide to continue further inside, despite the damage you take from the cold (you've been injected with Metroid DNA) you see Ridley (Who was supposed to be dead) frozen in a block of ice. Play farther into the game, go down the Main Elevator, and what appears to be Samus bursts into the shaft. Then it zooms right in on 'her' face, revealing that it's some kind of mimic. You later find out that this mysterious entity is called the SA-X, and that it's tracking you. You also can't even hope to kill it yet. You are told to run if you encounter it. And it does catch up with you. Then there's a boss called the Nightmare. It's been flying through the background of the damaged area of the ARC Sector, startling you the first few times it happens. Then you fight it. It has a creepy mask, and when you damage it enough the mask breaks, revealing its disgusting alien face that, as you damage it further, begins dripping.
Ni no Kuni is in a similar boat to Wind Waker in that it uses colourful anime-style graphics (specifically, it was animated by Studio Ghibli) despite it dealing with some surprisingly dark themes. The main character (who's only 13 by the way) watches his mother die of a heart attack only a few minutes into the game, and the eponymous 'other world' is very clearly a Crapsaccharine World with everyone living in fear of an Evil Sorceror who can effortlessly Mind Rape anyone who even thinks about standing up to him. Then there's Myrtle's story in the real world, which gives a surprisingly realistic view of how domestic troubles can traumatize kids psychologically. And Drippy dropsG-rated equivalents ofCluster F-Bomb all over the place.
One of the first notable instances of this in the main games is Pokémon Black and White, as well as its sequel Pokémon Black 2 and White 2; while not too dark for children per se, they featured many moral questions, a grieving, disillusioned champion, and a little girl literally killed in her sleep by nightmares, as well as the implied mental abuse and brainwashing of a young man, manipulated all his life and kept in an emotionally immature state (with a creepy theme and childlike "playroom" to show it, itself accompanied by creepy music) by the Big Bad Ghethis, with said Big Bad being quite possibly the most vile villain the main series has ever seen.
The Sea Mauville scenario in Omega Ruby and Alpha Sapphire, which also develops Professor Cozmo and Gym Leader Wattson, adds a large helping of material normally not used in kid's shows. It includes a Senpai Kouhai schoolgirl couple locking themselves into a side room for a private moment, finding abandoned documents narrating the rise and fall of the Mauville Mega Corp., an account of an employee's failing marriage from the perspective of a child, books about dealing with unemployment, debtors losing their Lopunnite Mega Stones to their debt collectors as collateral, and perhaps darkest of all, the harvesting of the life-energy of Pokémon as fuel, which is also implied to have led Wattson to forcibly tank all of New Mauville.
The Orregames were one of the first instances where the games truly started exploring darker territory, albeit Colosseum more so than XD featuring, among other things, a gritty, bleak Crapsack World of a region and a deadly practical, vile, ruthless evil team that would give Ghethis a run for his money. It shows that Colosseum's protagonist, Wes, being 17, which was practically ancient by Pokemon protagonist standards back then, and even now is still quite old.
In Pokémon Mystery Dungeon: Rescue Team, you have to save the world from an impending comet while fighting against a Gengar that accuses you of being a cruel traitor that was cursed for selling out his own Pokemon. In Pokémon Mystery Dungeon: Explorers of Time and Darkness, the plot is that you have to change the future because, as it is, it is a world of complete and utter darkness, where the sun never rises and the wind never blows. Besides that, innocent Pokemon get kidnapped, you have extremely freaky visions and, above all else, this whole game is a suicide mission. That's right. You die at the end and you know you're going to die. Chew on that. Finally, in the rerelease of Time and Darkness, they have mini-stories. And each one of those has a bad part, but the worst is probably in the last one, when one of the antagonists plans to suck your soul out of your body (think dementors), possess you, and go to the past in your body to convince people he is you. In the post-credits story, the Big Bad disguises himself as a good guy, visits you in your dreams, and tells you that the world is going to end, that it's all your fault, and that you and your partner should kill yourselves.
R-Type Delta is rated E. The final stage features depictions of fetuses as enemies to shoot. The ending for the R-13 features it becoming captured by the Bydo, with the final shot after the credits being of the ship enveloped by Bydo matter.
Rayman 3: Hoodlum Havoc has all sorts of sexual innuendos, Globox getting drunk, and the swamp hag using the word "pervert".
Rayman Origins is also well known for making the fairy girls (all of them) absolutely blatant sex-objects, complete with Hartman Hips, Jiggle Physics, Suave voices (albeit in pig-latin), porno-like music when you save them and the trailer shows Rayman using his hair to blow Betilla's skirt up...also, Betilla created him, so that technically makes him his MOM. Just to top it off, the manual describes Betilla as a badASS.
Some attribute the commercial failure of Shantae to this, among other factors. Shantae's cutesy, colorful graphics, goofy humor, being on the kid-friendly Game Boy Color, and a definitely present twinge of Girls Need Role Models certainly suggest it's a kid's game. The problem is, it's also strangely... sexy for something aimed at kids, and also more difficult than your average kid's game.
Sonic Adventure 2 features mass government killings, including a terminally ill 12 year old girl, Eggman using "Weapons of mass destruction", blowing up the moon, and putting a gun against Amy's head, and Sonic nearly dying in the equivalent of being chained to a bomb.
In Sonic the Hedgehog (2006), the main villain wants to destroy all of time and space, and Sonic gets murdered at the end of the game. (He gets better.)
Finally, Sonic Lost World features very dark dialogue such as "I long for death's cold embrace", "First you're contemplating genocide" and talk of skinning alive, and Amy and Knuckles get the life sucked out of them.
The two Tales of Xillia games are this trope in Australia, where they somehow managed to get PG ratings despite the first game having violent deaths and occasional blood in cutscenes and pretty explicit sexual references (there's jokes about bondage kinks) and the second game being Bloodier and Gorier, featuring huge amounts of blood in death cutscenes, terrorist attacks complete with masses of bloody civilian bodies (in one of the first areas of the game, at that), sexual references as normal and incredibly dark themes towards the end of the game. (The main character has to murder his brother to save the world.)
Undertale is intended to be family friendly, and it is, for the most part. However, should you decide to play through a Genocide route, the game reacts by turning into a grim, depressing slog, as you cut a bloody (or dusty, rather) swath across the underground, killing tons of lovable characters along the way—and unambiguously murdering a few! Unlike most of the rest of the game, none of it is played for laughs at all.
Kingdom Hearts is the tale of a group of heroes who journey through worlds based on Disney movies fighting cartoony monsters with The Power of Friendship at it's heart. Totally kid friendly, right? Well, the plot is actually quite complex to the point of Kudzu Plot, there is a lot of violence and some complex themes. Additionally, two games (358 / 2 Days and Birth By Sleep) involve the complete destruction of the friendship between it's protagonists and both have a Downer Ending. In Days, one protagonist dies while Birth By Sleep gives the protagonists a Fate Worse Than Death. The secret ending of Birth By Sleep makes them more bittersweet but even then it is unexpected for a series featuring Mickey Mouse, Donald Duck and Goofy.