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 Hooker Verse. 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. 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.
The police (and a couple of the Warblers) eventually find Wes and David tied to chairs—but Blaine is conspicuously absent, having panicked and ran off two hours earlier. Luckily, Kurt and Finn find him—unluckily, so does Alex, who locks Finn in the Navigator's trunk (spurring Carole and Burt to go help him). Blaine's Parental Substitute Greg is now the only one with any clue where Blaine is, since he, Dalton's dean, and another Dalton student are secret agents and Blaine's actual dad was too busy throwing a bitch-fit that he didn't find out earlier.
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.