Cenotaph zig-zags this trope as both played straight and inverted. On one hand Taylor's father is murdered by Bakuda on the other, Taylor dosen't spend the first month of her cape carreer fighting for her life against both sides of the law.
Series Five of The Lion King Adventures is incredibly dark, featuring the deaths of many beloved characters and countless tragedies.
The premise of People Lie is that Naruto was deeply affected by an act of violence during his youth, one that transforms him into a manipulative person with little interest in friendship. A running theme of the fic is how "some characters may have turned out even worse off if they had a father or mentor to look up to".
The story, Shell Shock is an incredibly dark take on military stories in the Frienship Is Magic fandom. It actually warns the reader: "This is seriously the darkest thing I have yet written. You have been warned."
The Discworld continuum offers the fanfics of A.A. Pessimal, which while written with a touch of Pratchett's absurdism, offer a darker edge to his fantasy world. The question from Pyramids, of what happens to luckless students who fail the Assassins' Guild School's Final Exam, is finally answered in detail that Pratchett only hinted at but did not give. According to reviews, this chapter moved one reader to tears. The Discworld country of "Rimwards Howondaland" is an expy of the old South Africa taken Up to Eleven, and has social institutions to match, as well as a paranoid and ruthless secret police - who are even called BOSS in the Discworld.
What makes this version of Freiza so terrifying is his motivation. In the original series, while monstrously cruel, Frieza's atrocities were mostly motivated by a desire to stay in power and t punish those who dared stand against him. In the abridged series however, it's made clear that Frieza commits his atrocities out of sheer boredom.
New World. A nice story about a teenaged boy and his adventures with pokemon, that just happens to feature murder, rape, and the apocalypse. The very first chapter features a Scyther beheading another Pokemon and then then being horrifically and disgustingly killed.
Let's not forget My Immortal, in which most of the characters have converted to Satanism "STANISM", Harry's scar is now a pentegram, and all the characters seem to do is Wangst around, cut their wrists, go to My Chemical Romance concerts, have sex, and proclaim how gothic "goffik" they are. The irony being that, for all its posturing, it's not nearly as dark as the actual later books of the series, for which see Literature below.
Pokémon has gotten a makeover with the advent of The Sun Soul, which combines a pointed Deconstruction with an Anyone Can Die attitude. So far, if the reviews and forum opinions are to be believed, the fandom approves.
Angel Island Zone. A retelling of the events of Sonic 3 from Knuckles' end of things. More blood, more tears, more drama, and more character development. And surprisingly, it manages to pull it off quite well.
You're Ready and You're Willin' by Hector Rashburn is in the same vein. Yes, there are two fanfics based on a t-shirt. Never underestimate the power of fandom.
Tiberium Wars manages to make the Command & Conquer Tiberium universe even darker than it already is, by virtue of introducing War Is Hell to show just how horrific the battles and weaponry in the setting really are.
Special mention should go to the "Rotten Dirty Bastard" fics. The special was Black Comedy dedicated to going to extreme lengths describing how much The Nostalgia Critic makes everyone's lives suck. The fics will either point out the flaws in these "happier lives" (like Iron Liz never meeting Linkara as one example) or have this heartbreaking sense of loss that makes you want to cry.
The Pokémon anime has taken on a much darker edge with Cornova's Poké Wars. Where the stories are set, all the regions have been ravaged by war. Not to mention, the stories are much more violent, cynical, grittier and much less idealistic than the anime it was based on.
For a show as innocuous as My Little Pony: Friendship Is Magic, there is quite a substantial amount of fan media with this in mind. Indeed, a great deal of the fanfiction is darker and edgier to some extent due to addressing more mature themes than the show. This is, of course, disregarding the stuff which is MUCH darker:
One of the most notable examples is Cupcakes, a fan fiction that has gained memetic status within the Brony community for its rather horrifying portrayal of Pinkie Pie and her cupcake recipe.
Another infamous one would be "The Rainbow Factory". The song it was based upon insinuated that pegasi did something to make pretty rainbows, but what, exactly, was left to the imagination. The fic spelled out in explicit detail the murder of foals too weak to fly.
Yet another example is Cheerilee's Garden, where Cheerilee deals with unruly students and the mane 6 (in the sequel) using certain methods. Arguably far more bothersome than Cupcakes, which may be why less people have read it.
The fanfic series Rainbow Double Dashs Lunaverse. It begins with a mild case of this, where the evil alicorn (here Corona, not Nightmare Moon) is able to remain free after being hit by the Elements and continues plotting to conquer Equestria. This amplifies over the course of the series, to the point where the season finale set at the Gala — in contrast to the original show, where the gala story was just about the six friends showing up and making a mess — has the Lunaverse 6 planning to commit high treason by poisoning a bunch of the nobleguests with a truth serum in order to destroy their lives/political careers.
The fanfic The Monster We Made is this trope. The story chronicles the last thoughts and actions of everypony as they are put to death by Alicorn Twilight Sparkle
Winter War takes the darkest elements of Bleach and runs with them. Bleach can get pretty violent, but it's usually contained in one-on-one duels, the only people who die are villains, and no matter how badly a good guy is hurt, they're unlikely to suffer any lasting consequences to it. Winter War throws that all out the window. Heroes die. Heroes will fight dishonorably or gang up on opponents if they have to. There are limits to what healers can do, and lingering injuries complicate daily life and battle alike. Aizen's Hollowfication experiments are shown as horrific and dehumanizing rather than being used as a source of power-ups. And the authors don't pull punches about the likely states of mind of people who've been on the front lines- or taken captive, or waiting back home for loved ones who are probably dead- for months.
Team Fortress 2 is normally quite a violent game, but always in a light-hearted and comedic way. Respawn of the Dead, on the other hand, is brutal and disturbing in its violence and very, very dark. Cat Bountry takes the personal quirks of the characters and expands them into full-blown psychosis. The result is actually quite good.
Cuanta Vida has moments of this as well, although in a very different way, largely by actually confronting some of the inherent Fridge Horror of the premise of the games. The fact that the characters are actually somewhat toned down from their portrayal in-game somehow only makes it worse. (For example, in the game, Spies are backstabbing bastards who relish killing. The main character spy, Bleu, actively avoids it.)
Alexandra Quick is this to Harry Potter, although in a way that doesn't go to the extremes of Darkfic or seem out of place with the mood of the original series. People do start dying in the first book though and there are some dark, dark plots in Wizarding America. Things get that way when you have wizards as government and wizards as terrorist with Blackand Grey Morality and you don't know which is which.
Part 2 of Clash of the Elements. There is little to no humor, some rather grim scenarios are brought up during Smithy and Dimentio's (Fake) backstories, including Betrayal, paranoia and the strong pursuit of a dream leading to the death of Smithy's closest friend, Dimentio casually mocking the love of Blumiere and Lady Timpani, along with his fabricated story that mentioned a pregnant Daisy DYING during an alien invasion. And that's not even getting into Chapters 21-29...
Game Theory is interesting in that while elements that were played for comedy in Magical Girl Lyrical Nanoha are now deconstructed for dramatic effect, and the lethality of the combat is notably higher, the characters are just as caring and morally upright as ever. In fact, the primary villain is more sympathetic. Which actually makes things worse,because Nanoha decides to help her. The ending , on the other hand, is actually happier than in canon. It just took a lot of effort and pain to get there.
Continuing with Nanoha fics, "Toward the World's End" starts out fairly light hearted with some cliche romance. It seems to just be so the author could get his OC with Nanoha... then, without WARNING, the entire world crumbles to dust and the only known survivors are Nanoha and Arthur, the OC of the author. Explicitly mentioned are the deaths of Arthur's mother and best friend, of Nanoha's childhood friends Suzaka and Arisa, and of course, Yuuno. Nanoha and Arthur wind up on a deserted island (Because these too many corpses of humans everywhere else) and are resigned to a hopeless life. At the end of the first story they bet their lives, not caring about the outcome, on a tiny [[Hope Spot]].
It's back to being a fair bit lighter in the folowing fics - however, the "everyone's dead" deal is still in effect
Horseshoes and Hand Grenades is set in the world of the friendship-based High School centered, Kamen Rider Fourze...except in this story, Gentaro was resurrected by an evil serpent and is causing mayhem as other Serpents start enacting Deal with the Devil themes with people who have died, more and more Kamen Riders get pulled into the madness, and at the end of the day, the bad guys are going to be claiming victory of some kind.
The Legend of Total Drama Island, a reimagining of the show's first season, achieves this effect by several methods, most notably by playing for drama certain incidents that the original played for laughs, and by replacing certain cartoonish elements of the original with some pretty stark realism.
Hivefled; on one hand, the entire universe isn't being destroyed and nobody's mind-controlled or in thrall to an Eldritch Abomination. On the other hand, the plotline was kicked off by a series of events involving the Big Bad couple raping thousands of teenagers to death.
Fallen King is one for the Yu-Gi-Oh! anime. Showing what could have happened if Yugi lost to Pegasus, it deconstructs the power of friendship that the series runs on. Joey realizes that the villains can and will use it as a weapon, and ultimately decides he, Tristan, and Tea must stop being friends to save the world.