Dark Fic / Pokémon

Due to the dark themes of the series, combined with the franchise being based on fighting, Pokémon has a large amount of dark fan-works.

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Anime

• Not as violent as other examples, but there is Ash's Coma. This fan theory suggests that Ash Ketchum was placed into a coma in the first episodes of the Pokémon series after being accidentally electrocuted by Pikachu. The theory goes onto suggest that several plot elements of the anime are actually the results of his coma-induced delusions.
• The Dark Side of Innocence is a James/Jessie fic where James is given a drug that makes him more violent by Giovanni. It features several graphic deaths, such as Giovanni being eaten by his drugged Persian.
• Denounce the Evils starts out as a canon-compliant Team Rocket redemption fic but it soon deviates into darker territory. It covers themes including mental illness, homophobia, transphobia, and childhood abuse. There's also some cursing and sexual references.
• Essence is a rewrite where a smarter Ash gets a Growlithe starter. The story has a more grounded approach to the Pokémon world that doesn't shy away from violence and dark topics.
• In Experimenting Fear, a young Nando is kidnapped by a Mad Scientist who studies people's worst fears and forces him to face his fear of losing his hearing because of his love for music.
• Infinity Train: Blossoming Trail is this in spades. While it would be darker than the anime by default given that the show it's crossing over with doesn't shy away from dark themes (mental health and some gruesome deaths in particular), the author still manages to ramp up the darkness as it goes on: Chloe and her companions end up in a Silent Hill-themed car where several other passengers have been brutally mind raped (and it's revealed that one of those passengers accidentally let a child drown), while the characters back home are dealing with the fallout of Chloe apparently running away — which includes one of them taking command of the Unown to exact some revenge against everyone he thinks is responsible, resulting in characters becoming suicidal and Goh in particular turning into an Empty Shell.
• Latias' Journey starts with the Ghost King destroying Latias' home city of Alto Mare and killing all of her friends after she spurns his advances.
• The anime itself glosses over the St. Anne incident, but Lost explores what it could have been Delia's reaction to her son's supposed death.
• In Mended, a 17 year old Ash finds out that Professor Oak is his father. Mended and its prequel Torn cover topics such as infidelity and love triangles.
• In The Myamoto Project, Giovanni plans on creating super soldiers using the likeness of Jessie's deceased mother.
• My Little Pumpkin is a Halloween-themed story that revolves around the relationship issues between Ash's mother and his distant father.
• Pathways. Just the cover art alone, with a bloody Pikachu looking especially nightmare-fuelish is enough to warn that this fic is quite dark.
• The multiple-novel-sized Pokémon Master claims to be "the first major Dark Pokémon fanfiction released on the Internet",
• Cornova's Poké Wars, comprising of multiple stories, is a particularly dark example that shows what has become of the world when Ho-oh decides to commit genocide against the human race.
• The Road You Choose is a collection of works based off of the Pokémon anime, with a few key differences: Aging, Misty, and Aura.
• Severance: Delia has been shot by Giovanni, who is out to kill her and their son.
• Team Rocket Roots is a comic bordering on Betrayal Fic that goes into depth of Jessie's Missing Mom Miyamoto and also involves Jessie turning on her friends.

Video Games

• In the oneshot Achilles' Heel, Lusamine's psyche is given more depth. Even years after the events of the games, she's still early in her recovery and is deeply troubled by her past behavior.
• In Anachronism, Gloria is sent back in time into an Alternate Universe after the Darkest Day causes tragedy. The character's personalities are depicted more seriously and they're a Dysfunction Junction. Hop doesn't take his defeats in stride, Sonia has a lot of issues behind her Desperately Looking for a Purpose in Life, etc.
• Chrysanthemums is a fanfic about how Cilan was raised a terrorist after being saved from death by Ghetsis. Years afterwards, he narrowly escaped execution after being arrested in Opelucid City.
• In the oneshot crack, break, shatter, Bede is killed in a raid battle. This causes many to protest raid battles as dangerous and worth banning.
• Easter Egg - Snow on Mt. Silver is a Creepypasta which gets quite dark in both the game, where the protagonist and their Pokemon freeze to death on Mt. Silver, and end up inside a hell-like dimension, where they meet Red and fall victim to an ambiguous fate, and outside the game, where the narrator’s brother is driven to temporary insanity by the unexpected horrors of what seemed to be a simple Gameshark code, and ends up giving up on the series due to the mental trauma.
• Forsaken begins three centuries in the future in a world on the brink of a world war. The world ends up destroyed, leaving the legendaries to survive on their own.
• Downplayed with Gym Leader Wiki. It is a fanfic where each chapter is the hypothetical Wiki page of an Indigo League member. Some of the pages reference things like suicide.
• The psychological tone of Only Flowers Fall is darker than the norm for the franchise. It's an alternate take on Sun and Moon's ending where Lillie doesn't forgive her mother Lusamine for years of abuse.
• The "Pokémon Black'' Creepypasta (these days it's usually dubbed "Creepy Black" or something along those lines to avoid confusion with the Generation V title) grants the player a Lavender Town ghost as a permanent party member, with the ability to curse enemy Pokémon and their trainers. At the end the would-be Karma Houdini protagonist is himself cursed by the ghost, resulting in a fade to black, a game freeze, and a deletion of the player's save file.
• Pokemon Light AU starts with Gloria being Driven to Suicide a year prior. A year later, Hop and Bede are still grieving.
• There's an urban legend of a hacked Pokémon game dubbed "Pokémon Lost Silver" that is pretty macabre, nightmareish and Mind Screw-y. It's unknown whether the game was real, or the guy who wrote about it just made it up, but it exists now.
• In Poor Rival, Red accidentally killed his rival Blue's Raticate in a battle, leading to Innocence Lost for Blue.
• Though it is also lighthearted just like Love Live! and Tokimeki Memorial proper, thus making it a zigzagged example, the Tokimeki PokéLive! and TwinBee series of fics can and do go into darker territory as well. Some examples include the destruction of an alternate Knothole Village (and possibly the rest of Mobius, at least that version of it.) at the hands of the Ultra Beasts, with the Knothole Freedom Fighters (excluding that universe's version of Sonic, Tails and Amy) as the only remaining survivors, PokéLive Eggman nearly killing the PokéLive! versions of Sonic and N in the "Ideal Hero" Side Story arc, just like Ghetsis nearly does to N in "The King Returns" episode of Pokémon Generations, and a possible future where Climate Change has wreaked havoc on most of civilization due to Yoko and Ellie losing the final battle against Eggman!
• Witchcraft is a oneshot where Red and Silver are half-brothers through Giovanni. The story is about how Ariana was a Glorifed Egg Donor in Giovanni's Darwinist Desire, and her relationship with her son Silver.