Being an Evangelion fic that tries to avoid the usual Fix Fic route automatically qualifies Aeon Natum Engel as this.
Another Evangelion fanfiction, Oedipus Ikari plays this trope painfully straight. When it looks like that Shinji and Rei are finally on course for a happy ending, Gendo orders Rei to break up the relationship which she does, albeit tearfully. Shinji reacts by stealing a gun and shooting Gendo in the headseveral times. Rei is pissed but manages to forgive him. It seems for a moment that a happy end is ahead once again, then the author screws us over again by having Rei confess her genetic origins to Shinjinote if the fanfic's title wasn't already self-evident: Rei was cloned from Shinji's mother and by Shinji having sex with her thrice, Unfortunate Implications arise. Cue Shinji becoming so squicked for a while that he can't even look at or touch her without retching. He eventually decides to apologize and make up with her... only to discover that she gave herself a lethal dose of anaesthetic so that her next clone can hook up with Shinji without prejudice... only for Ritsuko to confess that she destroyed all of the Rei clones an hour ago! True, the Evangelion verse is prime darkfic material but this is just plain ridiculous.
Both Syllables. Over the course of the series several main characters die, some planets are blown up, a main character is almost dissected, another character nearly burned an island to the ground, a lot of people die, and usually resolving one crisis results in several more popping up. Betrayals happen, horrific backstories get unveiled, and it just keeps getting worse with each update. That's not to say it's a depressing series and it's certainly not bad, but the whole thing pretty much runs on From Bad to Worse.
In the crossover fic, Amenaza this happens to Naruto. It starts off with his death and transformation to a Hollow. After that his afterlife takes the express service to metaphorical and literal Hell. By the time the fic reaches the main Bleach timeline, Naruto has jumped so far off the slippery slope and pass the Moral Event Horizon that nearly every other Hollow is terrified of him
Fairly English Story: After chapter 79, where Junpei's Persona starts burning him alive as long as he's concious and has to be put on life support and placed in an induced coma, It couldn't possible get worse, right? Right?
Based on the way things seem to be going in the Gears of War fanfic, Phalanx, it's probably about to get a hell of a lot worse, as if being shot down in enemy territory and having Dizzy Wallin for rescue wasn't bad enough.
Take control over Gekkoukan High School, secure the surrender of Minato Arisoto through use of hostages. Kill hostages if target fails to comply. Do not engage the target directly, nor attempt to subdue him or take him by force, he is a lethal and ruthless leader of the terrorist organisation known as Strega, going by the handle of 'Jin'.
The real Jin being the current Minister of Defence.
The Wretling fic TWE: The Next Generation it gets worse all the time. The two members of heel group Gen Now are eliminated in the Chamber meaning the Faces wins right wrong the new world champion joins them meaning they know have almost all the titles.
The Hetalia fanfic Family Ties. The small act of Scotland and N. Ireland leaving England and Wales escalates to WWIII. Many bad things happen, but then America and Russia start bringing out the nukes...
Just when you think life for the heroes of The Unity Saga can't get any worse, it does.
Son Of Apophis. The cast is trapped in their house. If they leave the army will assume they're guilty of treason and arrest them. If they stay they'll be assassinated. Whilst they're busy worrying over this, one of them is kidnapped. When they do to fix that the house gets burned down. Whether they were still inside or not is not yet known.
The pokemon fic Latias Journey. The fic's rating goes from being a adventure fic to become a really disturbing dark fic. The rating is changed from K+/T to M around chapter 35
The HookerVerse. Just when you think someone's been broken enough, it gets worse.
Even though some parts of it are less dark than others, and there is even some fluff here and there, Dragon Age The Crown Of Thorns is afflicted with this to a moderate extent. The Guile Hero dwarven noble protagonist even lampshades it, multiple times, like when talking to Trian and another time in one of the most recent chapters, after the psychic clash between the prince and the Archdemon made the latter smarter and more-selfaware. On the bright side, nothing seems too hopeless yet, and the fact that six full Origin wardens made it into the main cast should help fix things... probably.
Silent Sorrow, the final story in the Tamers Forever series. As it opens, Takato is already dying thanks to his Superpowered Evil Side overloading his body. Then, Shinjuku is invaded by a Digimon army led by Daemon, who is after the power of said evil side and is so insanely powerful that the only way anyone can even think to foil him is to let Takato escape to the digital world- so he can die before Daemon gets him.
Tengen Toppa Gurren Lagann is one work defied this trope, but some fics have this as an important point. See, The Rise and Fall of Captain Starlock makes this the entire point. It's kind of a novelization of how Simon became Captain Starlock, after Kamina's death (he dies in the first chapter, thanks to how Simon didn't know how to operate Lagann) and things just get downhill from there, Simon is nothing but a wreck of a man and still manages to be a competent antihero.
In the soul-crushingHunting The Unicorn, Blaine's entire life is an exercise in this. First, he has an estranged father—depressing, but logical. Then we realize how unbelievably naive he is. And finally, we find out that despite everyone's assumptions from his diabetes-inducing and chaste nature, Blaine's not a virgin.
That's not even getting to the actual plot involving Alex, Blaine's deluded stalker. He's first mentioned out of the blue by David, and we realize that this makes a lot of sense considering Blaine's insane obliviousness to love. It's not until the nineteenth chapter that he actually does something—namely, kidnapping Blaine, Wes, and David and locking them in his basement. Did we mention that Blaine got concussed and it's treated realistically? Which means that he isn't knocked out, but he was rambling incoherently for half an hour and now has no idea what happened or where he is.
When Alex finds them again in an abandoned hotel, Blaine tries to reason with him but it comes out semi-coherent at best. And then Alex tries to strangle Kurt. Luckily, Kurt goes berserk and starts pummeling Alex in turn. Their friends and Kurt's family finally find them, get Alex arrested, and take Blaine to the Blue Sun hospital. Where he tells his doctor Simon Tam about a conversation with Alex that the others haven't mentioned, and it's creepy enough to have him call Derek Morgan on the suspicion that Alex sexually assaulted Blaine and he can't express it properly.
During The Emiya Clan Christmas Special, the entire story is about the somewhat misnamed "Fellowship of the Sane" attempting to escape the madness that Altrouge has unleashed in the name of winning a bet with her sister for candy. Things start with them just trying to escape, but when that fails, they have to survive a Christmas Party that takes some of the craziest characters in anime, mashes them together with the clan, puts them in a house, supplies alcohol and sugar, and sits back to enjoy the chaos.
The author of that particular story even admits he was trying to find the absolute brink of insanity he could push the story to before finally wrapping it up.
The finale of Children of Time is fueled by this. (Warning: MAJOR spoilers ahead.) The way Holmes and Watson handle the dynamics of Watson's new marriage results in a horrific rift between the two, and Holmes seems determined to drive away the one friend he has left. Enter Professor Moriarty, Back from the Dead, with Colonel Moran at his side and Holmes and Watson in his hands. (With the new Mrs. Watson and Beth Lestrade running for their lives.) Did we mention that Time has frozen? Or that Moriarty seeks to corrupt Holmes into himself? Or that Holmes lets him? Or a major character death? Mm-hmm.
The Vocaloid fanfic From Concert to Chaos is absolutely packed full of this. The trouble starts towards the end of Chapter 4 and just keeps going downhill from there until the middle of Chapter 8.
Reconciliation takes place after Hanako's bad ending in Katawa Shoujo. It starts out being depressing enough, as Hanako has, out of guilt over her outburst at Hisao and Lilly in the bad ending, isolated herself from Hisao and Lilly for eight years, ending up as a successful but lonely author while they got into a relationship. The first major plot development is her hearing about Hisao's death.
This trope is enforced in The Infinite Loops. The admins in charge of repairing things don't like it when loopers forcibly end loops early, so any attempt to do so is punished by sending them into an even worse loop. Since most attempts to end loops come from the loopers deciding that the loop is bad.... it's a vicious cycle.
It practically defines the Mega Man loops. Right off the bat, the Mega Man universe was one of the worst damaged by the first Crash. The intial attempts to get the universe looping with Rock failed badly. The next attempt, with Roll, also failed badly. Then the admins tried Blues. Then they tried a Merged Loop, which went right through horrifically wrong and out the other side, with all four Anchors (the ones required to keep the universes intact) being dragged into a bizarre ritualised attempt for... something to ascend to god-hood. It ended with the universe they were merged with being outright erased from time and space forever, along with badly damaging the rest of the multiverse in the process. The Mega Man's next attempt at Looping was a do-or-die attempt, and if that failed, they've had been erased as well. They just barely squeak through, thanks to a Merged Loop with Sonic the Hedgehog's universe.
Misunderstandings: Peter Collins is transported to Equestria. Throughout the fic, in the short term, things go okay for him, but in the long term, things degenerate for him. Over the course of the story he's attacked by timberwolves, kidnapped to be abused and humiliated in a sideshow, escapes only to be hunted by ponies, nearly kills a pegasus soldier becomes the target of a frightened Blueblood who throws furniture at him with force to kill, faces an angry mob, badly injures himself on the stairs is nearly framed for eating a filly, attacked by rogue griffin soldiers, is teleported to the Astral Plane when one of Twilight's experiments is sabotaged, and the result of that is any pathway home as been blocked off, and the magic he has been absorbing will now build up inside him, until he explodes.
Sonic X: Dark Chaos starts like the original Sonic X, except Tsali attacks Sonic's world rather than Dark Oak. Then Satan himself steps into the fray, which rapidly escalates the conflict until the galaxy is torn apart in a war between demons and angels. And then an Eldritch Abomination appears, obliterates both sides, and nearly causes the end of the entire universe. Finally, the story ends with an entire race of Eldritch Abominations appearing and actually destroying (most of) the entire universe.