''Zenith, Darkness, Reverie'', a Death Note fanfiction, commences with a rock-climbing, Redditing nightcore fan locating a Death Note. It's destined to become a relatively light, humorous fanfic, of course. By chapter five (or approximately there), the protagonist is soliloquizing about obliterating humanity. By chapter fourteen, she has committed over one thousand murders.
The Lion King Adventures started off as a cute, comedic adventure series featuring Simba and Nala starting a romance as cubs. However, it evolved into a dark, gritty drama, rife with character deaths and tragedy.
"When 'Tamers Forever' was originally conceived, it was supposed to be a ten-story series mainly concerning a Takato/Rika relationship. It was supposed to be more of a romantic comedy, however, I realized my strong point wasn't comedy, as I unconsciously deepened and filled the plot with questions and secrets."
To give the man due credit though he never completely abandons the humour, in fact several scenes from later books are absolutely hilarious
Six Days The Animorphs Were Idiots begins as the crackiest of Crack Fic, with silly events happening and no real plot to speak of. Marco takes acid and hallucinates the brightly colored clouds on the book covers, Vissers 1 and 3 go on a date, Cassie forms a whale-worshipping cult. But the cast ends up hijacking a Yeerk spacecraft and travel to the Andalite homeworld, and the plot takes a turn for something that would not be out of place in the original book series. The sequel/prequel fanfic, The Other Attack begins with roughly the same level of serious that the first fanfic ended with.
Clash of the Elements Part 1 starts out with a little bit of humor and some light-heartedness you'd come to expect from a Mario game, but as time goes on and more details get revealed, everything starts becoming rather grim, culminating in the final battle where everything pretty much goes to hell and even when things are resolved it is a rather Bittersweet conclusion...
Taken Up to Eleven in the Series Finale, Black Rain, with an open that could pass for a slasher film, and Dr. Thunderstorm and Shadow possibly die at the end. Oh, and Slender Man appears. And he's a good guy.
God Save The Esteem begins by exploring the quirks of having Daria be raised by punks instead of yuppies. By the end, her father has nearly died, Daria has nearly been killed, a friend is in psychiatric treatment the school has been shut down for good thanks to a prank that Daria pulled on the cheerleaders, and martial law is declared, culminating in an epic battle of punks vs. police (with the National Guard preparing to move in).
The Intercontinental Union of Disgusting Characters is a series about exploiting the loopholes in the 1st Edition AD&D rules. But by the middle of The Sick Kids, well ... just try reading the final moments of Sick Sword's life without getting a lump in your throat. (Or the funeral for Ringman in The Intercontinental Proliferation of Disgusting Characters.)
My Little Alicorn starts out as a quirky comedy about Celestia being turned into a filly and Twilight and Luna having to put up with her antics while they also struggle to effectively rule the country until they can turn Celestia back to normal. Eventually though, things get much more serious and dark as we're shown how no one has forgiven Luna for her crimes as Nightmare Moon, we see just how self serving and manipulative the Canterlot nobility is, Blueblood becomes increasingly violent and deranged as he becomes obsessed with getting revenge on the Mane Six for the events of The Best Night Ever, and we get a firsthand look at how dark and graphic Discord's reign over Equestria, and the war to topple him was. And this is all beforethe appearance of an Ax-Crazy sorcerer who has murdered literally millions in his quest for immortality.
Getting Back on Your Hooves begins as a Slice of Life fic dealing with Trixie...well, trying to get back on her hooves with assistance of the mane six. While some serious moments, its still comical and Trixie's mess ups are presented comically. Then the Cutie Mark Crusaders decide to try and find a camping spot in the Everfree Forest, forcing Trixie and Fluttershy to go on a dangerous adventure to save them...and thenCheckerMonarch enters the story and pushes the plot in a direction more in tune with the two parters of the actual series.
The Nuptialverse: The first story, Post Nuptials, is a WAFF about the Mane Six dealing with the Guilt Complexes that resulted from not believing Twilight about the imposter Princess Cadence and their friendships coming out stronger for it. Then Families comes out and, on top of having to still deal with Spike's guilt and Pinkie's personal problems with her family, they also have to deal with a conspiracy to discredit and usurp Princess Celestia one member of which happens to be Scootaloo's total monster of a father. And that's not even mentioning the side story Metamorphosis, which explores Queen Chrysalis' incredibly darkStart of Darkness.
The MLP fanfic Trixie has a Problem, by the author of Twixie Genies, starts out as a comedic Slice of Life fic where Trixie is accidentally turned into a human, and the hijinks that ensue as Twilight struggles to cure her. Then Human!Trixie is kidnapped by the Apple Family, who in this story turn out to be cannibals.
And then comes chapter 6, where Applejack murders Twilight just because she tried to save Trixie.
Ask Jappleack began as a NSFW ask blog. After the success of Pony Dot Mov it started developing a plot. A plot which got progressively more dark, serious, and strange.
The Fan FicSonic Evil Reborn Zero. Already a Deconstruction Fic, the story makes a sharp turn southward at the start of the second arc when Sonic abruptly, for seemingly no reason, turns towards the dark side to join Eggman and Wikke (it's so abrupt even Eggman isn't prepared) and, immediately after, goes on a genocidal rampage through Station Square. Before this, it had been like a darker Sonic Adventure , with some chapters dedicated solely towards comedy and others towards drama, but this was the turning point where it remained dark. Amy's misery makes it worse.
When Innortal published his first time loop stories, the characters were just screwing around with their cannon. Then Saphroneth came along and started his My Little Pony: Friendship Is Magic loops, not only codifying the Infinite Loops setting but deconstructing parts of the premise, though the plot was still mostly the characters screwing around. The Mega Man loops open with their reboot being represented as a garbled datastream and an entire reality being obliterated, necessitating a three-way anchorship and traumatizing Rock, Roll, and Blues.
In Mega Man Defender Of The Human Race, post episode 5, the characters' morale and the tone of events in the story have taken an increasingly dark turn. This is best exemplified by the episode 10 epilogue, which is a nonstop string of tragic events.
Episode 11 is the darkest one yet, but has hopeful moments that become most prominent in chapter 11.
Happens across the entirety of the Mass Vexations trilogy. The first two parts are a relatively light-hearted romp through the Mass Effect series, with a sense of humor that wasn't afraid to tap into Medium Awareness at some points. The third fic ends with a Class X-2 Apocalypse How over Earth.