To begin, let's get the Elephant in the Living Room out of the way: A lot of doujinshi (which can be considered drawn fanfic) do this, both hentai and non-hentai. Steer clear especially of the hentai ones if your tolerance level for your favorite characters being raped is in any way low, as that's one of the least horrible things that'll happen to them.
Hate is an example of taking something that was already sad (Elysia's father's death in Fullmetal Alchemist) and making it absolutely horrifying. She blames Sheska for Hughes's death and turns to Envy for comfort, ending up as his lover. Elysia then tortures and rapes Sheska, causing a miscarriage, and tries (though ultimately fails) to kill her.
Possibly the ultimate example of a well-done Dark Fic is The Bitter End. It deconstructs the fanon " psychobitch" Akane into a real person with a real mental disorder, and then follows this premise all the way to its dark, bloody and horrifying conclusion.
Cornova's Poké Wars, comprising of multiple stories, is a particularly dark example that shows what has become of the world when Ho-oh decides to commit genocide against the human race.
There's an urban legend of a hacked Pokemon game dubbed "Pokemon: Lost Silver" that is pretty macabre, nightmareish and Mind Screw-y. It's unknown whether the game was real, or the guy who wrote about it just made it up, but it exists now.
Similarly, the Creepypasta "Pokemon Black" (these days it's usually dubbed "Creepy Black" or something along those lines to avoid confusion with the Generation V title) grants the player a Lavender Town ghost as a permanent party member, with the ability to curse enemy Pokemon and their trainers. At the end the would-be Karma Houdini protagonist is himself cursed by the ghost, resulting in a fade to black, a game freeze, and a deletion of the player's save file.
The Takotsuboya K-ON Trilogy, one of the more infamous works. You can find all three here (or on Fakku if you aren't fond of downloading). Be warned: this may send you into a depressing funk for quite some time.
The series had a bit of a dark turn in its final season, where a renegade magical girl tries to destroy the world and nearly succeeds. The Golden Queen of Shadow Galactica tells her side of the story, taking cues from the manga but featuring a dream sequence from the anime, and has what would definitely be considered a bad ending.
Deaths of the Senshi is quite good once you get past the squick. And they get better in end, so don't be too afraid.
Usagi Is Dead Hip Hip Hooray. The title only gives you the very barest inkling: it starts with an unspeakably horrifying tragedy that subverts the entire original show, and only gets worse from there.
The last Light is a short crossover in which the whole concept of the Sailor Crystals is given the Doctor Who treatment. Equal parts Tearjerker and Nightmare Fuel.
Damaged was a long-ago well-regarded darkfic in which one of the senshi is lost, presumed dead, in a battle with the Dark Kingdom. Lacking any explanation for what happened to her, officials turn their attention to the remaining girls, and their lives fall apart in different ways. But it's the ending that packs the real punch...
A highly popular yet unfinished Dark Fic is A Dangerous Pairing. The story features an evil version of both Usagi and Mamoru.
There are quite a few Naruto fanfictions which explore the whole children-as-warriors idea, as well as killing for money and the short life expectancy of ninjas. The only reason the setting of Naruto isn't already dark is purely because it chooses not to focus on such things, being a shonen series.
Atonement is a chilling description of a scenario in which a curious doctor delves into the case of a permanent psych-ward patient and regrets it. Naruto ends up in the psych ward by undergoing serious torture, losing one of his hands, going blind, having his chakra pathways destroyed due to forced extraction of Kyuubi, and ends up developing a split personality to cope: he ends up thinking he's Sasuke.
Fanfiction.net abounds with fanfiction describing Naruto's all-out, lifelong struggle to utterly decimate the Leaf Village because people hated him (he recognizes thispossibility himself). These are usually chock full of tales of him being beaten, burned, stabbed, mugged, occasionally raped (if the author is going for some real shock value), harassed, having his house destroyed, and generally just doing everything possible to make him kill everything forever.
The same goes for Hanabi, mixed with Bitch in Sheep's Clothing, due to her vague nature. However the manga suggests that she really is just a normal kid, and a nice sister at that, and the anime follows that through.
Ten Thousand Fists involves him getting an Omnitrix filled with anime characters in place of aliens. And you know its a Dark Fic when Chapter 1 has Iruka tortured, mutilated, and killed with the same happening to Naruto, who only lives due to a Deus ex Machina. Then we find out he suffers the usual gamut of beatings, burnings, dog maulings, rapes, etc. And somehow it manages to get worseonce Kakashi shows up.
Naruto Veangance Revelaitons, was said by the author to be an attempt at a dark fic, and there is no shortage of terrible happenings in there, including mass murder, rape (by "heroes" and villains alike), and the end of the world.
Lonely Kagamin. The True Companions have split up, they've all gone to college, and Kagami is stuck in a depressing rut in which she no longer socializes with anyone. Until Konata walks back into her life... only now Kona-chan is a suicidally depressed loner who cuts herself. They fall in love and sleep together... and then Kagami wakes up and realizes it was All Just a Dream and goes back to her painfully stagnant life. (Which, itself, was All Just a Dream, and Kagami wakes up to find Konata next to her. Apparently, the Downer Ending was an April Fools joke meant to depress the reader.)
Lonely Kagamin? How about Bulimic Prostitute Kagamin?. That's what you'll find in Lucky Star Blues.
Another popular subject is the conflict between North and South Korea. North Korea is usually portrayed as a hardened womansoldier whose goal is to force her brother South Korea to accept communism—whether he likes it or not. The conflict usually is portrayed as bloody and tear-jerking, and both Russia and America have no qualms about taking advantage of it.
Many fics involving colonialism, especially in regards to the British Empire, plunge straight in to darkfic territory in a brutal analysis of the implications of colonialism for the personified countries - anything regarding the Opium Wars is practically guaranteed to be this trope.
There are also quite a few darkfics based around the end of Prussia or the Berlin Wall, which usually involve him being kidnapped and tortured/raped by Russia for a few decades. Any fic about Russia and the Soviet countries is practically guaranteed to have him do horrible things to them, esspecially Lithuania, Latvia, or the aformentioned Prussia.
One particularly disturbing example is the Fusion Fic doujinshi Drifting Classroom, a horror tale void of any of the series' humor, optimism or light-heartedness. It involves the school, with everyone inside, being sent to a barren world. They split into factions over whether they should attempt to find a way home or try to start a life in the new world. People start dying, Osaka finds a gun in a paper bag and begins killing the other girls, Chiyo winds up getting the gun but Osaka stabs her in the throat. Then Chiyo sees Chiyo-Daddy after she dies, who is actually God or something, then wakes up to find it's All Just a Dream and everything's fine.
There is a Hentai doujinshi (links will not be provided - Brain Bleach is expensive) which revisited Osaka theorizing about what would happen if Chiyo got kidnapped. It's a Hentai. Do the math.
I'll Be On The Road Again, in which Kaorin realises that she can never have Sakaki, and ends up killing herself by driving her car into a wall. Short and eerily In Character.
Yomi: Tomo-chan, my best buddy in the whole world, wait for me so we can 'team up'! I'll introduce you to my new friend, Mr. Spiky Bat! He's been wanting to meet you for a real long time. I think you're going to become real close!
Differing Paths, in the genre of "Tomo-as-badass-cop" fics. Not entirely serious, but contains severe, near chapter-to-chapter Mood Whiplash. This is the kind of thing that goes straight from a hilariously meta Lucky Star crossover, to Tomo torturing Kaorin.
BetrayerS is something of a household name for Nanoha darkfic.
The two 'Karakura Cops' stories. It places the Bleach characters in a police force setting and the Espada are a terrorist group who brutally murder almost the entire cast. Apart from containing cannibalism, suicide and child murder, it actually starts off as a light-hearted comedy.
Alive takes the verse's base darkness several steps further by introducing one more factor: the real reason why Rei is so subservient to Gendo is that he's sexually abusing (and by abusing I mean brutally raping) her on a constant basis and she's too scared for her life to do anything about it. Even worse, the last chapter implies that Ritsuko is well aware of it. It's also sadly a Dead Fic which means the darkness won't get resolved.
Taboo ParallelCrosses the Line Twice: Asuka and Rei are being blackmailed to perform depraved and degrading sexual services for two guys, drugged, raped, and filmed. Due to the drugs, both girls behave like nyphomaniacs. If they refuse, the footage will be released with express intent to ruin Asuka's reputation. Then it kicks into even higher gear, with the reveal that Yui was the one who supplied the boys with the drug fo her own reasons. And the final strike: Rei is innocent in all this. She had nothing to do with it, Yui had her raped only for appearances.
Similarly, Zero 2: A Revision. It starts off fairly light — and then the Emperor nukes a city to try and kill the Digidestined. It lightens up for a while after that, but then really darkens during the last third or so of the story, as DevimonMind Rapes Davis to create the being known as Darkheart, who spends the next dozen or so chapters curb-stomping and tormenting the Destined. And while that's happening, there's a three-wayinvasion of the Real World that devastates Tokyo and ultimately leads to several character deaths. And one of the factions that invades the Real World is/are an Expy of the Flood.
Negimaru, a Dark Fic for Mahou Sensei Negima! made by the same people who made Drifting Classroom above and Evangelion RE-TAKE. It's about Chisame’s alter ego Idol character getting beaten by her fellow classmates in Internet popularity polls so she schemes of a plan to destroy their reputations online by using her *ahem* cosplay skills. Her plans succeed a little too well, and... let’s just say she gets too involved in her plan...
Also made by Studio Kimigabuchi is a Sgt. Frog doujin titled Hikari No Kuni. Which shows a dark version of an alien invasion from Keron.
Respect is a What If?Smile Pretty Cure! story that examines what would happen if timid crybaby Yayoi Kise made a contract with Kyubey in order to stop a bully from tormenting her. Needless to say, things go downhill quickly.
Based off To Love-Ru, "To-Love-DEATH" is all this. Taking a silly romantic comedy like To Love-Ru, allow the characters warm your heart, then get destroyed with zombies!
The Puella Magi Madoka Magica fanfic Persephone's Waltz manages to be even bleaker than its notoriously depressing source material, with an incredibly detailed exploration into someone's slowly collapsing sanity and the horrible things that people can be driven to in desperate situations. About halfway through Sayaka brutally stabs Homura to death (it doesn't stick) and it isn't even the most horrifying thing that happens.
Archie and The Punisher met halfway in their unlikely 1994 crossover (not a Fan Fic) in which The Punisher tracked an Archie lookalike to Riverdale with orders to apprehend rather than kill him. The original pitch involved Archie hiring The Punisher to kill a psychopath who murdered his entire family, but this was considered too dark.
Archie Comics' Sonic the Hedgehog crossed over with, of all characters, Spawn. Naturally the latter was toned down in keeping with the former's (mostly) kid-friendly atmosphere, but still...
Disney Ducks Comic Universe got on dark story titled The Adventures Of Gyro which involve the friendly inventor Gyro Gearloose going disturbingly insane and doing some truly despicable things to other characters (from kidnapping and starving their children to burning down their home) with complete lack of motivtion and while having a deadpan expresion on his face which makes the entire thing extra eerie (even if some parts are clearly played for laughs). DarkFic indeed...
Eugenesis is an incredibly dark continuation of The Transformers, one that plays the horror of war utterly straight, and subverts or even outright averts some of the usual tropes of Transformers fiction. Characters, even important or beloved ones, can die horrible and sudden deaths. And that's before we even get to what the villains of the piece do.
Margo_Kim's "The Value of Strength" has the premise "what if Steve Rogers is secretly a complete sociopath?" and ruthlessly reinterprets the events of the film and its predecessor and predicts the future actions of the character based on that.
In Steve He Saved for Last, Tony flips a coin every New Year's Eve to decide whether to spend the year good or evil. This fic is what happens when he flips evil.
"Draining the Oasis Dry features a Bruce Banner and Tony Stark who are secretly evil, and, as a couple, are sexually aroused by murdering people in situations where they've ostensibly attempted to SAVE them.
Rhombus's The Seven Hunters has the premise "What would happen if Littlefoot and his friends were suddenly turned into carnivores?" and it plays the premise to its logical, horrifying conclusions.
The Lord of the Rings fandom has plenty of these, many involving Elves and Ho Yay. However, one fan fic stands out as being extremely disturbing: And These Pearls That Were Her Eyes. A story based on The Silmarillion segment about the last king and queen of Númenor, it's a dark tragedy about spousal violence and rape. (Not that The Silmarillion isn't pretty dark to begin with.)
If you ever wonder why the obvious plot bunny of "what if Aziraphale was the demon and Crowley the angel?" hardly ever pops up, read The Sacred And The Profane. It proves that the only way to pull this off without completely abandoning canon characterization is to deconstruct the traits that would otherwise be out of place when on the other side. Aziraphale's affability becomes the facade Zirah assumes to convince others (and himself) that he's really an angelic soul when he's not casually offingpeople, and Crowley's tendency tobe not so evil around Aziraphale is translated into Caphriel's inability to let go of his love for, and what passes for a relationship with, Zirah. Armageddon is still being averted seems to take most of the edge off... and then an exception to the canon-established Everybody Lives outcome occurs: Caphriel kills Zirah to get over his unhealthy love for him, so neither of them gets a happy ending. And all because an angel had the wrong thought in the wrong place.
A good number of fics about a Second Apocalypse that the characters have no hope of averting, Crowley and/or Aziraphale being punished for averting Armageddon or their love, or Crowley revealing that his Noble Demon personality was an act all along and making Aziraphale suffer for his misguided trust/love. Some of them are competently written, while others plunge straight into Deus Angst Machina territory.
Due to its nature, The Phantom of the Opera is rich with possibilities. The Phantom is a Stalker with a Crush, who has been watching a little girl for years as she grows up (hidden behind her mirror, no less), who has a history of assassination and dark magic (among other things), and whom most of the fans still want to see get the girl. Ironically, this goes back to the original interpretation of the character, prior to the the musical version, which made the Phantom Lighter and Fluffier.
Many, manyHarry Potter fanfics. Before book 7, most were of "What if Voldemort wins" variety (Cycle of the Badger, for example). After that, they mostly flesh out the what was happening with the rest of the wizarding world during the book. Also the First War is quite popular.
Oedipus' Flower, where Harry's parents survived and Voldemort wasn't around, so Harry himself was the villain. By the end of it, Harry had killed his own brother and almost killed his father, plus raping his mother and sister.
Hogwarts Exposed is something of a Dark Fic, full as it is of rape, pedophilia, torture and bodily functions; the author disagreed with himself as to the extent to which this was intentional.
The Padfoot Tragedies series, a "what if" story except the what if in question is "What if Sirius killed himself in his sixth year following years of abuse from his family, pedo!Fenrir Greyback and Hogwarts head girl, and Bastard Boyfriend!Remus? And that meant the Voldemort never fell? And then Sirius somehow comes back from the dead 20 or so years later?"
How do you make a magical world even darker? By crossing it over with Hellraiser in "Evil Be Thou My Good". It's actually a bit of a subversion as things end relatively happily... so long as you are Harry or one of his friends. The Dursleys, Death Eaters, Umbridge... yeah, things don't go well for them.
The Paper Doll Kindergarten. Remember Nessie (or Renesmee Carlie, if you prefer), Bella's super-quick-growing genius vampire baby? Well, Nessie isn't happy. Sadly, this fic is no longer available for whatever reason.
"What Dreams May Come", which just applies the "vampire hypnotism" found in so many other works of vampire literature to Twilight, while simultaneously showing Edward in the most creepy possible light. Mind Rape ensues.
Nessie inspires a lot of this. There are two companion fics, called "Seven" and "Eighteen" which deal with two possible interpretations of her strange aging.
For a different look at the horrors of imprinting, For You, I Will is an incredibly dark work that has Embry imprinting on a traveler named Melanie. Everyone promptly accepts it as True Love like in the books... except Melanie is nothing like the other "wolf girls", and starts using the imprinting bond to force Embry to do all sorts of horrific things with her. By the end of the fic, Melanie is forcing Embry to help her brutally sodomize and murder brown-haired women. Jacob and the other werewolves manages to figure this out, but the story ends with Melanie ordering Embry to secretly kill them all, so they can't interfere.
Neil Gaiman has written a The Chronicles of Narnia darkfic called "The Problem of Susan" about Susan after her siblings are killed so they can stay in Narnia. It involves White Witch/Aslan sex. He also wrote Snow, Glass, Apples which makes "Snow White and the Seven Dwarfs" much darker by telling it from the Queen's point of view and making Snow White the villain.
The A dance of Shadow and Light series by Ocadioan takes the Inheritance Cycle and makes it significantly darker and more brutal. Especially as of Phonenix Fire, where the body count in the first ten chapters alone reach above 250,000.
Live Action TV
The infamous Mighty Morphin' Power Rangers fanfiction Agony In Pink, the far-too-long story in which the original Pink Ranger, Kimberly, is kidnapped, raped, tortured and snuffed by Lord Zedd in very graphic fashion. Some believe it caused an "international incident" (if being mentioned as a reason for filtering a site counts as such) and may have been the reason that fanfiction.net stopped allowing NC-17 stories.
Smallville, being the origin story for The Cape, Superman, was fairly light until Bizarro showed up, and more so after Doomsday entered the picture in season eight, but Dark Fics in the cheerful early seasons is quite common. Crisis, for example, with graphic descriptions of sexual assault, torture, attempted murder and copious amounts of angst.
Battlestar Galactica (Reimagined) has, among others, The Long War. Rather than chase after the Galactica and search for Earth, the POV fleet decides to remain at the colonies and keep fighting the cylons. Despite a few victories and poor cylon tactics, they are slowly suffering from attrition and the cylons are starting to learn. The fleet's commander is slowly going insane and the overall outlook looks even bleaker than the television series.
Doctor Who is almost custom made for this. Even beyond the Doctor being a well-baked angst muffin with psychological scars so deep you can fit entire lost civilisations in them, the legions of vicious, dangerous and destructive Aliens and Monsters that have been featured, the sheer potential of a vehicle that can appear anywhere in time and space, and a universe that is Always Doomed all combine to contain endless possibilities. Fans have not ignored any of this.
On a more subtle note, Psycho Savior, qu'est-ce que c'est? features a pretty dark take on the Ninth Doctor, who was never exactly a sunshiney kind of guy to begin with. Fortunately, the writer never forgets that the Doctor is, in fact, a Big Damn Hero, which keeps the story firmly on the side of pretty damn good.
Day of the Barney, which depicts Barney the Dinosaur as an evil immortal overlord bent on conquering the world (his first and only successful attempt involves inciting every child in the world into a riot against everyone else) with a major case of hypocrisy, not being afraid to murder in graphic manners while maintaining his sickeningly sweet personality. Oh, and his backstory holds him responsible for killing the dinosaurs, corrupting Caligula, unleashing the Black Plague, rescuing Adolf Hitler and leading Those Wacky Nazis to Anne Frank.
Remember the Star Trek: The Next Generation episode with many Enterprises and a reality where "Federation has lost and Borg are everywhere"? Well, there is a fanfic about it here.
Many Mash fics focus on Hawkeye Pierce struggling to adjust to life after the war and often end with him being Driven to Suicide. Arguably justifiable, as he always was a little bipolar and had a complete psychological breakdown in the series finale that caused him to be committed to a mental hospital. Fanfic writer Meredith Bronwen Mallory has some disturbingly well-written darkfics on Fanfiction.net. Mostly Slash Fic, but all haunting and brilliant.
iCarly can get some pretty bleak fic. It's usually based on Sam's potentially abusive mother, or the potential for a Sam/Freddie relationship to go horrifically off the rails and end up with Sam physically abusing Freddie (often including rape).
In the Carly/Sam fandom, fanfics relating to Sam's behavior pop up, especially self harm (cutting, drugs, alcohol abuse, etc) related ones.
In one fic, the gang holds a segment on iCarly where anyone can suggest a website and they'll visit it. Someone links them to various shock sites. Needless to say, the kids are scarred and it doesn't get any better from there.
There's a popular type of dark fic called JDA in Scrubs fan fiction. In them, JD is often suicidal, abuses drugs, and has cancer in a few of them.
Blues Clues of all series has at least one. It's a subtle, realistic take on the series and it delves into the fact Blues Clues isn't real, or doesn't appear to be to most.
Stargate SG-1 has the Eurydice Verse, in which the damage doesn't reset itself after every episode. The author probably thinks the characters should be a lot more screwed up than they appear to be in Canon.
Believe it or not, fanfiction.net's small cache of Everybody Loves Raymond fanfic consists almost entirely of Dark Fic, which is pretty surprising for a sitcom. There are a couple of fics where Debra cheats on Ray with Robert (including one where the result of this action is both Ray and Amy becoming embittered, dark souls who join forces to plot revenge, if I remember correctly), one where Marie has a heart attack and the other characters stand around sneering and laughing at her instead of calling an ambulance, and one that features teenaged versions of Ray and Debra as angst-ridden Emo Teens who spend an afternoon cutting themselves.
How I Met Your Mother has an entire livejournal community of darkfic — an impressive feat for any fandom, let alone a sitcom. Most of them involve various main characters getting into abusive relationships (either with each other or with one-shot or original characters, but most often Barney/Robin), extreme genre shifts changing the setting from comedy to crime/drama or thriller/horror multichapter stories, or subjecting one or more of of the characters' pasts to a Cerebus Retcon, again, usually involving abuse. idioticonion is one of the fandom's most prolific darkfic writers.
Although Supernatural is pretty dark to start with, some fanfics manage to make it worse, usually through a lot of torture and rape. One fic springs instantly to mind when Evil!Sam decides to make Dean his sex slave, mostly through raping the living daylights out of him, all in a world where Hell had taken over. And any fic that takes place in the Alternate Universe shown in "The End", where the Sam and Dean fail to stop The Apocalypse from happening and Sam agrees to be Lucifer's vessel.
A Sweater Stitched in Lies is a darkfic of The Cosby Show (yes, really) featuring murder, attempted murder, insanity, meth addiction, domestic and child abuse, and lots of sex. Sondra goes insane after Elvin and the twins are murdered in their home (or she murders them, it's not clear), and everything goes downhill from there, with the family falling to pieces while trying to cope.
High School probably takes the cake. All the characters are teenagers. Pig-pen gets Violet pregnant. Snoopy gets rabies, kills Woodstock and Linus and infects Sally with the disease. Schroeder is a gay psychopath who kills Lucy, kills the rabid Snoopy, and then admits his love to Linus as he dies. Peppermint Patty and Marcie are lesbians with AIDS. Charlie Brown is emo and commits suicide.
The Weapon Brown series is a twisted version of the Peanuts characters All Grown Up in a post-apocalyptic world. Nearly everything that's ever been on the funny pages makes a cameo, but notable major characters are "Chairman Horns" from Dilbert, "Warden King" and The Wizard from The Wizard of Id, "Anne" from Little Orphan Annie, and "Pops" (from Thimble Theatre, but you know him better as Popeye). And then there's CAL-v.1n.
It probably won't take long for someone to find a Calvin and Hobbes dark fic, such as Camp Nightmare. Calvin is signed up for a day camp which has a really cheery atmosphere and people dressed like clowns... then Calvin and Hobbes discover a room full of the corpses of partially eaten children and it goes all downhill from there.
Calvin and Hobbes invites a whole category of Dark Fic, dark cartoons, etc., in which Calvin comes to realize that Hobbes is really a stuffed toy, and the live tiger was a figment of his imagination.
Little Shop of Horrors is somewhat dark at times on its own, but somewhere on Deviant ART, some fanfics are, instead of a surreal musical romantic comedy from the 80's based off of a dark comedy from the 60's, quite dark and dramatic, such as Seymour's Nightmare.
The original Dino Attack line was just a couple of guys with high-tech vehicles and over-the-top weaponry fighting mutant dinosaurs in a city for no particular reason. Dino Attack RPG manages to take the vague premise and run it into a much Darker and Edgier drama. In the RPG, the mutant dinosaur rampage isn't just affecting a city, but it's a global catastrophe ( planned by the Darkitect). Instead of just four guys, there are over two hundred people fighting to save the planet, many of whom have depressing backstories, psychological issues, and character arcs with tragic consequences. The rest of the story is filled to the brim with death, destruction, genocide, drugs, alcohol, sexism, smoking, homophobia, child abuse, murder, betrayal, and torture, just to name a few. There's even an alternate ending that ends with an Earth-Shattering Kaboom and everybody dying. Did we mention this was based on a LEGO line?
Prison Island Break makes most Dark Fic look like a cookbook right from the start, taking the best part of the franchise to prison. We're talking Sonic the Cop Killer here. It's not just the way that the writer seems to find a new way to violate basic human rights in every chapter. It's not even the way that despite the torture, the graphic rape, the murders, the savage bloodshed and the strong drama, they successfully maintain the character's core personalities. It's the way they continue to give their readers the gut-churning feeling that they actually Did Do The Research.
Rockman: the Robot War: Creative liberties with the characters aside, the result is a deconstruction of the games: Wily starts out trying to prove that removing humans from industry would destroy mankind, aligns with the Human Supremacy League, a robot hate group/terrorist organization, but is ultimately driven insane from his efforts, why the human military doesn't get involved in the fighting, the robot masters are mass produced, and Rock is creative with his weapons, like using Rolling Cutter to decapitate Iceman.
One can't mention "Mega Man" and "Dark Fic" in a single sentence without thinking of The Protomen first.
Mega Man X, being a Darker and EdgierSequel Series, has a lot of potential for dark fics, considering that most of the enemies are driven insane by a virus, there's a near genocidal war going on and Zero's . Darkfics usually center on torture/rape by Mavericks, fanatic between humans and reploids (usually where reploids are badly mistreated), and the horrible things that could happen if Zero ever truly went evil.
Why The Rainbows Make Me Cry has its' fair share of tragic character backgrounds. This time around, the focal character turns out to be the Scout, explaining why he tends to get upset over a certain line of Spy's dialogue... and dear god, the explanation is just heartrending. Sometimes, it just doesn't pay to be a Karma Houdini.
Tales of Symphonia is very far toward the idealistic side of the sliding scale, full of bright colors and empowering morals. But since almost none of the characters have any living family, the Exspheres that give the protagonists extra power are not only made from human souls, but those souls are implied in some cases to be still conscious, and you have the option of killing the Handsome Lech, the canon seems practically designed to inspire Dark Fic.
There are numerous "Organization 13 running a brothel" fanfics, which generally focus on "LOL SEX MAKES MY FIC EDGY." One fic, oblivion, is inspired by Toni Morrison's Beloved, beginning with Axel having killed the rest of the Organization and being haunted by Roxas, who is violently unhappy about his state. Most people focus on the unsettling plot and Roxas The Angry Ghost, but the aching dynamic between Axel and Roxas has been commented on by more discerning readers.
One of the better examples of this genre is All_the_Roads_We_Have_To_Walk All The Roads We Have To Walk, which tosses Sora through a keyhole into a "shadow dimension" of sorts and charges him with finding a way home. Despite being a darkfic, the series maintained much of the tone of the original series simply by taking the darkest moments of the games and using them as a baseline for the overall tone of the series; it isn't dark so much as it is darker, and much closer to the center of the Sliding Scale than the main series. Granted, there are some very dark moments (just to name one, Halloween Town comes with its' own HeartlessExpy of Pyramid Head) but the situation never feels completely hopeless, and the series comes highly recommended even for people who usually avoid darkfics like the plague.
In-universe example: Paper Mario: The Thousand-Year Door, at one point, involves Luigi going off on his own journey through the Waffle Kingdom, which is, if anything, rather comical (as his helpers will tell you). At some point, a book of his travels is published, which surgically removes any comedy his journey may have had and replaces it with overly-dramatic Purple Prose.
Touhou games are based on Excuse Plots of some Youkai being dumb or just plain bored and end with a Spot of Tea or some similar meeting of all the main characters, heroines and "villainesses" alike, but for every WAFF or Slice of Life fanfiction there's a darkfic to counter it. The mountains of Fridge Horror and being a definite Crapsaccharine World don't exactly help, humans almost completely at the mercy of the incredibly powerful youkai that can (and have) put the entirety of Gensokyo at risk on a whim, and despite their appearance a lot of characters are derived from and/or have the potential to be some truly horrifying creatures.
Almost every Western fan will know what you're talking about if you mention A Bad End. It starts with an Ax-Crazy Kaguya declaring war on Gensokyo, and escalates from there. It is running on Rule of Funny - no one cares about anyone dying and it runs on Black Comedy.
Reimu Surrenders and is Destroyed is considered one of the most repulsive HentaiDoujinshis to be released about the series (once again links will not and should not be provided) which involves a Brought Down to Normal Reimu encountering a lowlife in an alleyway. Once again, it's a Hentai. Do the math. Graphic for it's eleven-page length (a safe way to put it), to the point that several hentai sites don't even allow it.
A Scarlet-Stained Memoir is a finished CYOA that takes a darker view of the Touhou universe, particularly the Scarlet Devil Mansion and it's residents.
One of the more well written dark fics in the Soul Series is an as yet completed fic called The Pitfalls of Madness featuring the main character Cassandra slowly going insane.
The normally comedic Space Quest has at least a couple. The Middle of the Night deals with Roger not quite being the idiot he appear to be. Burn, Xenon, Burn follows Roger's son from the future, the horrific implications of Space Quest 4, and portraying an extremely unflattering depiction of Xenonian society.
The Sims, due to how players can essentially create their own stories in the game, has a large roster of Dark Fics. The Sims Wiki's Fanon Portal features a lot. One in particular, "Night of the Living PlumbBob," stands out. It features Sunset Valley being victim to a zombie outbreak, many characters dying, such as Erin Kennedy, Gwen Glover, Agnes Crumplebottom, and CORNELIA AND MORTIMER GOTH (implied), and The Government choosing to destroy Sunset Valley completely.
Raccoon is a Sly Cooper kill fic (Dimitri brutally tortures and murders Sly), which, to some, has to be read to be believed. The author apologizes in advance to anyone who gets nightmares after reading it.
Homestuck has more than a few dark fics due to the sheer amount of Fridge Horror it has. Most commonly focused on the doomed timelines, but several AUs about a dystopian non-sgrub Alternia, a post-game world where either trolls or humans have enslaved the other species, or just canon continuity stories with a lot of rape, death, Wangst and abuse. One such fic is Reprise, which is essentially 30-odd chapters of Gamzee Makara being horribly raped and tortured by his ancestors, the Grand Highblood and the Condesce. The sequel, Hivefled, is similarly dark (though less graphic) and expands on the setting and characters' history in ways which serve largely to make things somehow even worse, for example Gamzee only being one in a very long line of victims, but at the same time maintains the potential to Earn Your Happy Ending.
The Worm fic Cenotaph both plays this straight... and inverts it. On one hand Taylor's father is murdered by Bakuda and she almost dies on the other, Taylor dosen't spend the first month of her cape carreer fighting for her life against both sides of the law.
A disturbing amount of That Guy with the Glasses fanfiction is Dark Fic (the other half is Crack Fic), mostly due playing crazy comedy characters for drama and the challenge of still keeping their personalities intact is more fun than it should be.
The Hooker Verse doesn't do too badly either in this department, either. The only difference is that it replaces war with, well, the internet personas either whoring themselves out, becoming pimps or paying for said whores.
The fiction blog Hitherby Dragons tries this with many of its entries, spanning from The Smurfs (undergoing the Trail of Tears), to My Little Pony (during the apocalypse), to Glow Worm (as a demon, fighting a doomed battle against worse horrors), to The Lion The Witch And The Wardrobe (the heroine dies early on), to stereotypical high school Magical Girl stories (the magical girls are the Four Horsemen of the Apocalypse). In the bittersweet style of Hitherby, some such stories (like the one where Teletubbies are suffering eternal punishment for their sins) turn things around on the reader again and manage to end on an uplifting note, while others do not.
A popular meme on tumblr involves "genre swap" — i.e., taking carefully-selected screenshots of a particular fandom and arranging them and moderately manipulating their tint, exposure, brightness, etc to make them fit a completely different genre. You've got some dark-to-light — Dexter as a romantic comedy! Breaking Bad as a Rogers and Hammerstein musical ("Albuquerque's Alive With The Sound Of Dealing")! — but others are light-to-dark, such as Glee as a horror film, How I Met Your Mother as a murder mystery (involving the murder of the eponymous mother), or Tangled as a psychological thriller.
The Burbank Confession, where toons experience prejudice from humans, to the point that one who is seen AT ALL is shot with a turpentine bullet. Dot flips off a cop, bloody battles ensue, BUGS FRIGGING BUNNY DIES, and many other equally pleasant things happen.
Bonds, in which the Warners, years after the end of Animaniacs, along with the rest of the cast of the show and a few characters from Tiny Toon Adventures and Looney Tunes, confront a mystery regarding the death of Slappy and the disappearance of toons in North America. It also features a very unique view of the world in which not only Animaniacs, but all cartoons co-exist. Oh, and also has romance.
Transformers-related Dark Fics are not uncommon. Unsurprisingly, they tend towards war stories.
For example, fan-comic "War Journal" ends with an outnumbered, outgunned group of Autobots preparing to make their last stand... A Decepticon Army Ending, if you will.
There are a number of Teenage Mutant Ninja Turtles Dark Fics. The general public may look upon the Turtles as kid friendly fare thanks to Adaptation Displacement, but the fics in question hearken back to the days of the original comics, which got pretty damned dark and violent. Yoshi's backstory alone was nowhere near kid-friendly. There is a Fanfiction.net community devoted to these darkfics, many of which are quite well-constructed.
Mutant Ninja Turtles Gaiden, a fancomic that deals with the four turtles growing up with psychological problems after a horrific incident, wrapped up in a mystery regarding a new turtle (who has his own set of issues).
Kim Possible darkfics are not uncommon either, usually involving the return of Ron's evil side, or Kim turning to evil. One featuring Kim holds that the good/evil switchingdevice will make a moderately good person moderately evil, and a very good person very evil. Having been through it, Kim tortures Shego with scalpels and pliers for her amusement. It's well written, but (obviously) really unpleasant.
Paragon, pictured above. It's a very well done horror story that involves Josh Mankey cursing Ron with the ability to see the dead. His ultimate goal is to use Kim as a vessel for his mother's spirit, since she is the paragon of perfection in his eyes. The story ends with Ron's spirit in Josh's body, so Kim can finally be with him without worrying what the rest of the school thinks, but the experience has left them so psychologically damaged that they decide to kill themselves.
There are fan made webcomics of both Nickelodeon's Rugrats and Doug, the latter dealing with Doug seeking revenge on Skeeter for raping and killing Patty, after which it became So Bad, It's Good.
Despite its generally lighthearted mood, the show has proven itself to be incredibly prolific when it comes to fics regarding torture, experimentation, and dissection. One of the most famous of these is Phantom of Truth by HaiJu. Told from Maddie Fenton's perspective as she observes the infamous Phantom in a government facility, the fic contains several instances of electrocution torture and in one chapter includes an incredibly detailed description of the severing of Phantom's hand. Another one is Lab Rat by AnneriaWings. Not for the faint of heart, this 20K+ fic is one of the goriest dissection fics out there.
South Park seems to practically hemmorhage darkfics. For an example of a Cartman centered dark fic, we have Playing God, in which Cartman matter-of-factly and brutally murders Kenny (yeah, we know, but it's taken seriously this time) as an experiment to see if he'd come back after being murdered in cold blood. Everyone being in-character makes it worse.
Avatar: The Last Airbender fandom breeds darkfic almost as much as it does shipping. While vastly varied, it can generally be divided into three main groups: a) From before the series begins, speculating on what a century long war would do to the world, b) During the series, exploring the minds of what are essentially Child Soldiers and the implications of a lot of the on-screen nastiness (such as the main characters' impressive body count), as well as the depredations of the Fire Nation, or c) Set after the series, deconstructing the Happily Ever After ending on the entirely reasonable basis that a lot of the Fire Nationals aren't just going to accept peace, and the rest of the world isn't going the let them go unpunished. Alternate Universe Fic, for example the Fire Nation winning the war, is also popular.
Anything serious by marvel26 can give chills. Especially when the Fridge Logic behind it all makes sense. His story Manifest Destiny is a chilling depiction of the Dark Side of Aang's love for Katara to it's extreme. And by the same author is His Father's Son, a story that explores Zuko as Fire Lord Post-Series.
The ATLA Wiki's fanon portal features a large number of Darker and Edgier sequel fics, AU fics, and prequel fics. A:TLAR gets some attention purely for being recognized as being one of the closest to an unacceptable (by ATLA wiki rules) R rating, without being out-and-out graphic. My Own Savior is particularly dark.
For some reason the author gave it a T rating, but Lady Noir is creepy, especially given that in The Legend of Korra, Aang is dead and Katara is alive.
While Invader Zim isn't exactly a cheery series to begin with, it usually addresses dark and serious issues (the main character is trying to enslave and/or genocide humanity, after all) with relative sarcasm or surrealism. Fanfiction writers, on the other hand, often take these more seriously, which is relatively easy to write considering the Crapsack World in which the series occurs. Often this includes a.) Zim destroying the world and feeling bad about it afterwards, b.) Dib killing Zim and feeling bad about it afterwards or c.) Zim or Dib simply realizing how horrible their lives are and killing themselves.
There exists a Dark Fic, aptly (ironically?) named "Twilight on London," that manages to turn much of the Disney/Don Bluth Mouseworld on its head and rework it into a Godfather-like tale taking place in 1800s London, replete with sex, beatings, murders, and all-around Canon/character-breakage.
It is pretty much natural for Chip 'n Dale Rescue RangersFan Fiction to be Darker and Edgier than the show itself. Yes, it is about cute and fuzzy little rodents, but these cute and fuzzy little rodents are quite elaborate and multi-dimensional characters in a rescue and crime-fighting team. Many fans feel that Disney never really fleshed out the potential of the latter. So must CDRRFan Fiction sends the Rangers into way bigger and more dangerous cases than the show and drives them to their limits and beyond. While not taking anyone Out of Character, building up on established character traits instead, it tends a lot more into action-adventure and drama. Most CDRR fics that aren't Darker and Edgier are parodies on something because there are hardly any Slice of Life fics.
Under The Bridge is about Gadget's long-lost twin sister who wants to kill Gadget because she thinks their father rejected and tried to drown her because she was born as a one-armed albino and not a cute little blonde like Gadget. After several unpleasant encounters, the latter opts for drastic measures to save herself and her friends. It was eventually given a MSTing co-written by author John Nowak himself.
The Rescue Rangers fanfic tradition already started out a great deal Darker and Edgier than the show itself when its very first real Fan Fic ever written, Rhyme And Reason, was released in 1996: A mysterious villain sends Chip on a dangerous quest all over the city to find his teammates whom said villain threatens to kill by sunset — and puts through an individually tailor-made physical and emotional wringer.
The Lost Tales of Fantasia combines every Disney story (every single one) into a single world, while answering some Fridge Logic questions with Fridge Horror. Why are Peter Pan's ears pointy? Tinker Bell was his mother. She almost died in childbirth due to the size difference. Why is Captain Hook such a bumbling figure compaired to the original works? He's holding back a little because Peter's his son. He only wants to kill Tinker Bell, and only because he's slowly been driven mad by the forces of Hell. By the way, Hell is Wonderland, and the Queen of Hearts is an Eldritch Abomination. Oh, and the story takes place during World War Two. So Hitler has a Villain Song.
The brilliant Teen Titans fanfic Joker's Wild shows what happens when you take a mass murdering psychopath like The Joker and put him into a light hearted series like the Teen Titans cartoonverse. It's moments of horrific slaughter are matched by twisted humor. Not surprising considering it's about the Joker.
Unsuprisingly, Jimmy Two-Shoes is lending itself well to this. Being a kids show that takes place in Hell, it was asking for it.
Go to a Daria fan site and look for fanfics written by the "Angst Lords" - a number of Dariafic writers who really turn the screws to the characters in the show. What makes the majority of these fics really dark is that they're also really well-written.
Most Wanted (since deleted) includes Mr. Krabs dying (implied), some mysterious knocking and a wolf kidnapping SpongeBob and throwing him in the back of a truck in chapter 5 (including Mr. Krabs almost being killed in chapter 2), glass getting pushed onto SpongeBob in chapter 6 leading up to when his arm almost gets sliced off.More outrageous, it's rated T.
Felony deals with some mysterious disappearances that have been going on in Bikini Bottom in the past few years. Spongebob is getting worried, but he and Patrick decide to go to Goofy Goober's for some ice cream. They end up getting drunk, just like in The Movie, and get into a barfight. Spongebob is taken to the emergency room, but is ok. Patrick, however, is nowhere to be found. It turns out Plankton captured Patrick and took him over to the Chum Bucket. Patrick also learns where all the citizens have been disappearing, and what Plankton's been making his chum out of.
Jeftoon01 has drawn a series called Twisted Princess wherein various Disney Princesses are portrayed in macabre styles, ranging from creepy to plain horrific. Each drawing has an accompanying short story that details how the princesses came to share such dark fates. He is also working on a similiar set, Twisted Fairies, with describtions connecting fates of each disney Fairy to larger Myth Arc. Here y'go.
Among the increasing amount of The Amazing World of Gumball dark fics, there's Rise Of Darkness and The Orb Of Corruption both of which are very dark, but especially the latter.note By the end of Chapter 5, hundreds of innocent tourists at a theme park have been massacred and/or corrupted and turned "horribly evil", Gumball's family have almost been killed repeatedly, and poor Larry has died in a fire at a convenience store.
Regular Show fan fiction Asleep in a Blizzard pairs Benson with a snow globe named Evelyn, who suffers at the hands of an abusive boyfriend and dies with Benson's child (how does candy dispenser sex work?) and Benson kills said abusive boyfriend.
Somebody actually had the guts to write a 3-2-1 Penguins! darkfic titled Down the Gurgler. It's about a human named Gina who finds out in a terrible way about what happens when a player gets sent down the gurgler. It doesn't start out so bad, but as the fanfic progresses, it gets a little more graphic than what would be seen in the actual show.
Street Sharks Redux is what happens when Street Sharks is re-written to include all the Fridge Horror. Events made considerably darker than in the series (such as the experimentation and brainwashing of Slammu), and it delves into a lot of the psychological horror a person would face if they found themselves mutated against their will and forced into hiding while worrying about their loved ones.
The Adventure Time fanfic Spindle, Spire takes the series' Cosy Catastrophe and turns it into an After the End setting that would make Fallout crap its pants. If you don't get bitten by a zombie, eaten by diredogs or have raiders do... things to you, you'll eventually rot from the inside out anyway, the only semblance of civilisation is under threat from a previously unknown brainwashing monstrosity, and the main characters are inflicted with every manner of Body Horror. This eventually culminates in an ending that might be called bittersweet if you tilt your head and squint a lot.
Gravity Falls has a ton of then. Given the show's nature, this isn't really surprising.
It Runs In The Family is about Gideon's sadistic cousin, Cashmere Gleeful, getting revenge on the Pines family for getting Gideon arrested and put in jail.
The same author wrote another story called The Seven.
The fan sequel The End of a Nightmare continues the story and explores the psychological damage everypony felt since Rainbow Dash's death a year earlier.
Party of None is based on the same plot (written with Cupcakes in mind) and has the same basic idea, but it isn't as violent (Pinkie Pie doesn't kill her here, and it has a better ending. In fact, with the exception of Rainbow being a little shaken up and her hair being ruined, it ends pretty much the same as it did canonically in "Party of One".).
The much-loved flash game Story Of The Blanks is somewhat unusual among dark fics, as despite being significantly darker and more gruesome than the show, it sticks pretty close to its themes and tone.
Several Ask A Pony blogs depict a rather horrifying alternate Equestria, where among other things, Rarity is evil, Berry Punch is a pathetic, drunken, incestuous single mother (and her daughter has a porn addiction), and Pinkamina is even more psychotic than usual, with Scootaloo as her cheerful sidekick.
The Pony POV Series is on the Earn Your Happy Ending side of things, and ultimately a lot of circumstances have improved from what they were at the beginning... but there is a long list of good reasons why this version of Discord is considered the most horrifying the fandom has ever produced.
Fallout: Equestria is immensely darker than the show it's based on. Featuring the aftermath of a magical apocalypse, mutated monstrosities, murder, rape, cannibalism, racism, attempted genocide, fates worse than death, its darkness is matched by its length as it is one of the longest fanfics in the Friendship is Magic fandom (recently surpassed in both word count and darkness by a spin-off by the name of Project Horizons) leading to it being also one of the most well known. A plethora of other spin-offs continue the darkness the original created.
Heavenly Turmoil, where Celestia is psychologically tormented by Discord to the point of being driven batshit insane. Also manages to work in some pretty hefty Mind Screw, with later chapters making it increasingly hard to tell what's real and what's in her head.
The story My Little Slave has Fluttershy kidnapped and turned into a sex slave. Then it turns out to have been a rape-dungeon roleplay scenario, initiated by Fluttershy herself. Even with that knowledge, some of it is still more than a little squicky.
The Secret Life of Rarity depicts Rarity as a serial killer dating back to a self-defence killing in her foalhood, though she's portrayed as a Woobie, Destroyer of Worlds, as she clearly hates that she has so little control over herself, as well as the impact she ultimately has on her friends and family.
Solitary Locust is the story of Twilight seemingly turning herself into a changeling via use of changeling magic. It includes detailed descriptions of injuries - including Twilight's horn nearly being ripped off of her head when she is attacked by a mod - as well as thorough physiological issues with many characters.
Pages Of Harmony can be noted for many of the same sort of reasons as The Secret Life of Rarity. Involving Twilight brutally murdering her friends to get their Elements, it is extremely disturbing and graphic, full of Mind Rape, Ax-Crazy Twilight (and Rainbow Dash as a result of said Mind Rape) and very detailed scientific procedures, and thus is NOT for you if you can't handle that.
The Monster We Made is an exercise in minimalist horror. Each chapter with the exception of the last two is only 1000 words in length, but boy does it pack on the dark. The plot features the darker side of Twilight's transformation into an Alicorn, as she brutally slays each and every one of her friends. Each chapter makes you live the last moments of a different pony, so be prepared for some major Tear Jerker moments.
The Path of Absolution: Punishmentstarts with literally the entire cast bullying the CMC into suicide over the events of "Ponyville Confidential", and it only goes downhill from there. The fic has two endings, one an Earn Your Happy Ending, and the other a Downer Ending where the Mane Six perform a Senseless Sacrifice, leaving their friends and loved ones alone and traumatized. The sequel is even worse.