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Given the large number of variations on the same stories, there's quite a bit of this within the spinoff comics as well. One of the more common interpretations in runs of the first gen and its remakes is the common Fanon theory of Blue/Gary being Oak's Unfavorite while his grandfather favors the MC appears quite often. Other runs paint him as a flat-out Jerkass, while others split the difference for a Jerkass Woobie.
Another frequent point of variation: how gym leaders and other trainers respond to death on the battlefield. Any given gym leader could be portrayed as a professional who has accepted death as a natural consequence of battle, a friendly foe who's honestly shocked at seeing their opponent's pokemon die, or an utter Jerkass who gloats and rubs the loss in their face.
In almost any Ruby/Sapphire/Emerald run you read, Norman will be interpreted as a trainer who is so obsessed with Pokemon that he neglects spending time with his family.
Fake Difficulty: YMMV, but due to the random nature of the game playing a big part of the game, the Nuzlocke challenge tends to involve more grinding and random deaths.
Straw Man Has a Point: There's something to be said for N's claims — that pokemon battles are cruel, selfish, and only result in pokemon being hurt — on a normal playthrough. On a Nuzlocke run, he's pretty much right.
Fridge Brilliance: Squirtle and Charmander's little slap fight at the start of the Fire Red run makes more sense once you've seen their Origin Story.
Growing the Beard: The Ruby run was good, but rough around the edges. The Fire Red run saw a general improvement in the art, dialogue, characterization and plot, and was an even better series.
Also in Emerald, Archie is a hippie, and Maxie is highly competant - he just wants to give land-dwellers a place to stay whenever Archie manages to flood the world.
And then there's Tate and Liza... even their Pokemon were freaked out.
In Platinum, Barry Stanley is an abusive boyfriend who tries to keep Shrinking VioletDawn Bern cowed.
Harsher in Hindsight: In Hale's comic, Hale tells May that she should kill herself. Guess what she tries to do later on.
Funny Aneurysm Moment: May was treated as an Ineffectual Sympathetic Villain and her threats of murder aren't taken very seriously, even when she kills grandma Winstrait. But then she finally manages to kill Django...
Ship-to-Ship Combat: Of a sort; the fight was between Hale/May and Hale/nobody.
Fridge Brilliance: Giovanni is startled when Candace disguised as a Rocket greets him with "Hail Giovanni!", because he's not the leader of Team Rocket any more. She blew her cover.
Moral Event Horizon: Candace breaking and entering into the Olivine Town lighthouse, now a shrine to honor Jasmine who sacrificed herself to allow the rest of the town to survive, by way of Forretress' Mirror Shot to get the badge, considered a sacred object by the survivors, was viewed as this by some people.
Memetic Outfit: Played with during her Pearl run, as Lily remains the heroine and Gary the rival, but they wear the familiar outfits of Dawn and Barry.
Ship-to-Ship Combat: So much in her Pearl run, between Lily/Gary and Lily/Lucas, that she had to threaten to holler at the mods in the opening post of her Sapphire run. Gary won, if you're interested.
Kynim's Nuzlocke Runs[]
Ensemble Darkhorse: Kynim wasn't really expecting all the love Mimi got from the instant she joined the team.
Moral Event Horizon: Lyrax's Gold run immediately establishes the rival as a Complete Monster when he steals both of the leftover starters, apparently just so he could tell Lyrax "Don't follow me or I'll kill one of them." He does.
In Azza's Run[]
Complete Monster: God,Gary and his Charmelon. See the Moral Event Horizon trope.
Moral Event Horizon: Charmeleon (and his trainer as well) make it clear they're well over the Complete Monster line when Raticate argues that the murder of innocent Pokemon was completely unnecessary, and demands to be released from the team. They do so, but then Charmeleon claims that since Raticate is now a wild Pokemon, he can do whatever he wants, and very brutally murders Raticate as well.
Complete Monster: Villain Protagonist Melvin from the dead comicChronicles of Rolthar, whose mission is to kill every last Pokemon trainer in Kanto and take their eyes as trophies. He has a Freudian Excuse, but it's flimsy (his brother lost an eye in some sort of war involving Pokemon training, and Melvin is trying to get revenge for him) and wasn't fully-explained before the comic went dead, and Word of Artist says he's not supposed to be sympathetic.
The Unnamed Protagonist from Pitch Black is a terrifying, evil, sadistic protagonist. From the beginning it's established that he's NOT a good character, (Considering we see his first activities IMPALING POKEMON ON HIS PICKET FENCE). From then on, any Pokemon he catches he forces to fight and brutally murder his friends and family and sees them nothing more as tools, even going as far as to KILL his own Pokemon. Basically, he's an even worse version of Paul. His Oshawott, Icarus, MAY be just as bad.