This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Latias' Journey
The fanfic's prequel, Your Secret Admirer starts off rather pleasant with Latias receiving gifts of affection from the Ghost King which culminates for her hand in marriage. Latias politely turns him down. Discovering she has a crush on Ash, he proceeds to destroy Altomare, Shedinja murders Bianca and Lorenzo and then destroys the Soul Dew. The Ghost King then sends a letter to Latias, proclaiming when he finds out who her true love is, kill him and then marry Latias. When they actually meet, Latias is unsurprisingly pissed, even when he realises he overreacted.
The concept that Team Rocket has agents in every society in the world, and any friendly person could really be evil. And that they use Shadow Pokemon due to their alliance with Cipher.
The Prison Balls that Latias carries with her for several chapters contains several Ax-Crazy Pokemon, including the Wigglytuff that co-starred with Psyduck in Cleavon Schpielbunk's film, who went insane and murdered all the cast and crew save Psyduck following its bad reviews.
Chapter 5 is a bloodbath. Fearow and his army of birds massacres the Winged Fortress, murdering countless Pokemon including children. Latias witnesses a Skarmory decapitate a young Delibird, who she turns into liquid metal when she freaks out. After Pidgeot is killed, Latias unleashes her wrath by vapourising every Pokemon in sight.
Seviper, Dustox and Cacnea as Shadow Pokemon, turning them into Ax-Crazy maniacs and literally screaming bloody murder. Cacnea continuously attacks James throughout the fanfic until her Heel–Face Turn later on.
Grovyle is captured by Team Rocket and becomes a Shadow Pokemon for a time.
Deoxys' entrance into the fanfic. Crashing down as a meteorite, he obliterates Big City and then murders the Pichu Bros. because he can.
Deoxys himself is Nightmare Fuel incarnate in this fanfic. Initially introduced as a destroyer of worlds and Mewtwo's nemesis, Deoxys is recruited as a member of the Unown's Chosen for the apocalypse and sent to the moon to meditate until further notice. However, Deoxys begins recollecting the shards of his memory core and remembers he is a Dark Lord and it is his destiny to destroy reality. He begins a bloody nightmare fueled war against Earth, ripping out the souls of countless people and torturing the souls for eternity. Deoxys then unleashed a zombie virus across the world, turning most of the population into the souless undead.
Suicune's rape and torture.
Mewgle is a delightfully horrible master of nightmare fuel. A parody of Mew, a Moogle, and the Killer Game Master trope, Mewgle starts off as a relatively harmless but taunting NPC. Contact with Deoxys turns him into a psychotic Reality Warper (at least within his RPG software) that can turn into a Eldritch Abomination with wings made of fire. Delights in torture and violence, while still maintaining an upbeat nerdy attitude and is one hell of a sore loser.
The whole chapter of "RPG Redux". All the major Team Rocket members are placed in an Eldritch Location of a prison and told by Mewgle to get out alive, before he devours Cassidy in front of them. To make matters worse, unlike the previous game Mewgle played, the participants actually die. Butch, Hun, and Annie are all eaten at some point, Attila becomes Half the Man He Used to Be thanks to Giovanni, Oakley is trapped in a Saw-like death trap which kills her via lethal injection, decapitation and being set on fire at the same time, and the Iron Masked Marauder gets his head eaten by a living mask. Jessie and James survive, but Jessie is corrupted by Deoxys so she can see her mother again, and poor James becomes Dark Latios' chew toy.
Deoxys ripping Domino's head off.
Meowth's transformation, becoming a giant undead Persian with no eyes, a Cheshire Cat Grin, and his internal organs on display. And all the other Team Rocket trio Pokemon go through equal And I Must Scream transformations - Chimecho looks downright terrifying and malevolent but is still the same playful, child-minded creature it always was.
Lugia is tricked by Suicune into killing his wife and child, believing they have become Deoxys' minions, when they were only Shadow Pokemon and could have been saved. Then, they become Deoxys' undead minions.
Although he deserves it for massacring the Mirage Kingdom, General Hanson's execution is pretty horrible, considering it is aired on television and Misty and Togetic watch it.
Project Hero - A well-intentioned project made by Mr. Ford to create superheroes, but most are turning into violent sociopaths and others turning into evil monsters. The machine used to transform people into superheroes is powered by one of Deoxys' crystal shards, explaining why most become The Psycho Rangers. Used to forcefully turn Ash into the violent psycho Alpha Ranger.
Alpha Ranger is the soulless version of Ash, an Ax-CrazySuper Soldier of a Psycho Ranger who plans on murdering all of his loved ones just For the Evulz. He then proceeds to kill all of Steven's Pokemon - Claydol via Megaton Punch, Metagross' face is melted off by supersonic punches, Aggron's gut is ruptured and he is used to flatten Lileep. He then shoots May's Munchlax dead, who absorbed electricity beforehand, causing the power to rebound and kill Psyduck and Misty's Luvdisc. By the time Latias has arrived, Alpha has killed all of Lucy's Pokemon, Crobat, Steven, castrated Brock, and deliberately ignored May. What an asshole.
Mr. Ford uses Project Hero to transform into Shining Ranger, who is just as bad as Alpha, but wants to kill all humans to destroy the very concept of evil in humanity. His first victim is his own so Harrison.
Infernatrice beats the heck out of Charizard and RIPS HIS WINGS OFF! This forces Latias to turn the almost dead Charizard into a Charmander again to keep him alive.
Poor Drew, who was the Pokemon equivalent of Tuxedo Mask, has his head blown up by Deoxys.
Lance and Drake get eaten by a horde of Glalie after a Snorunt informs them that they were the ones that had apparently sent Ash and Latias to kill them.