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- In the Yu-Gi-Oh! fanfic Not the Usual Kaiba, Mokuba seems to be turning into one.
- In Naruto Veangance Revelaitons, an ending that the author's former stepbrother wrote has Edfred and his boyfriend Muskoka restore the cast to normal, enabling them to kill the hated main character, who easily fell into several Mary Sue categories.
- In the Mai-HiME fic Perfection Is Overrated, the main cast goes up against a group of foes called SUEs, who represent typical Mary Sue types, with powers symbolic of the Mary Sues' impact on the plot, such as a fundamentalist Christian with the ability to reduce the effectiveness of her enemies' powers. Miyu accidentally becomes one by killing Akane's Child and resulting in the death of Mariko, whose powers made her extremely popular on campus and enabled her to become Akane's most important person instead of Kazuya.
- In the Sailor Moon fic, Super Sailor Chibimoon Eradicates all Mary Sues!, the author had Chibiusa, with the help of Helios, eradicate various Mary Sue archtypes found in the Sailor Moon fanfic community.
- Limyaael wrote The Game of the Gods, a The Lord of the Rings fanfic that has Morgoth playing a game with Varda where he creates Mary Sues and places them in Middle-Earth while his opponents use logic and the rules of Tolkienian canon to kill them.
- The Redwall fandom used to have these. It was headed by a weasel named Kelaiah and a pine marten.
- The Epitome of Randomness came up with their own interesting take on the genre. Specifically, a whole organization of children dedicated to the field. Introducing the Sue Slayers!
- Narutaki in Kamen Rider Decade is an odd canonical one. Hellbent on making sure Decade does not enter any worlds except the world of Negatives. He does things ranging from rallying the entire world of Riders against him or at one point summoning an makamou to stop him.
- Self-Extraction is a story about a Badass Normal former BattleTech Pilot who joined the Agency to stop the intrusion of the Dream Maker, a person who lets people live out their fantasies in other dimensions which have in some way caused trouble. Sues range from crushing the toughest folks in Street Fighter, attempting to kill Barney the Dinosaur, and becoming an all-powerful demon god just because the person wants to create a CrapsackWorld with several worlds completely empty.
- The webcomic Mary Sue Academy has a group of Mary Sue Hunters as villains (sort of).
- Lynching ITP is a set of Play-by-Post Games which combine this with Mega Crossover, usually directed at the worlds of Twilight or Inheritance Cycle, though it has a tendency to turn into an Ultimate Showdown of Ultimate Destiny with the Sues in the background.
- Anti-Cliché and Mary-Sue Elimination Society is Exactly What It Says on the Tin. Most Sues hunted by the group are from made-up fanfics, but Sues from real fanfics are, at the request of the author who owns them fair game. (The society hinges on the belief that Sues are often Old Shames of whoever first designed them.) Unlike most, the Society offers rehabilitation to captured Sues, and a few members of the Society are reformed Sues themselves.
- The Protectors of the Plot Continuum could be argued to be the Trope Codifier for Mary Sue Hunters, as whether or not they started it, they definitely popularised the idea. Different from others in that it has its own shared universe.
- Dr. Clef (the character, not the author) of the SCP Foundation has a reputation for "decommissioning" Reality Warpers... most of which are terrible Mary Sues written by people who don't know any better.
- He Who Fights Monsters kicked in pretty hard. Once Clef's fellow Sue Hunter, Dr. Kondrikai, was found riding The Dreaded SCP-682 like a bull, they knew they had gone too far and began retconing Mary Sues instead of decommissioning them. Clef's writer has also written a sorta-retcon which leaves to the reader's imagination whether Clef's feats of badassery are real or an unremarkable researcher's records corrupted by an SCP-732 outbreak.
- Ensign Sue Must Die - In Ensign 2: The Wrath of Sue, because of the Enterprise's actions in the last one, the crew of the Enterprise (and The Doctor) travel the multiverse to contain the many Mary Sues that spawned in it with Pokéballs. However, it turns out that had been Sue Prime's plan all along, to get all the Sues in one universe and weaken the fabric between dimensions so she could come back.
- Pony POV Series:
- It has a somewhat unique, dead serious example with the Blank Wolf. As the Guardian Entity of the timeline, it's meant to erase things that shouldn't exist, which includes Mary Sues. As a result, it can No Sell their OP abilities. However, in this universe, Mary Sues are Played for Drama as creation-threatening Cosmic Horror level beings created by unknowing Shadows Who Make that attempt to hijack existing stories and twist them to revolve around them, and most of its victims are creations of the author for the story including the Big Bad General-Admiral Makarov rather than ones he perceived as Sues.
- However, not all of the Sues are made by the Shadows Who Make (who are basically the embodiments of the fan communities' aspect of creation). Makarov is revealed to have been a living storybook character created by Pandora, the Token Good Teammate of the Draconequus (and Discord's sister.) It was all a complete accident and she helped put down her creation (who was in their prior form, an alicorn princess.) She sealed it Pandora's Box and things were okay... until the Hooviets got their hands on it.
- Furthermore, the Blank Wolf is by no means perfect at his job per say. For the longest while, it was stalking Shining Armor.... Turns out Shining Armor is the split between two timelines (between a good and bad ending basically) and he is basically living his life to reach up to that point. From a cosmic stance, he was created by the Alicorn version of Twilight Sparkle and embodiment of Hopes, Dreams and Happy Endings. Shining does lure the Wolf to defeat Makarov, but he is still hunted until the Wolf is put down by Cadance, an Alicorn as well. He does come back as a pup to help the CNC during Discord's endgame (where he is named "Blanky.)
- Pinkie Pie packs an Anti-Mary Sue bazooka. In several fights, Rainbow Dash asks her to use it, but she claims it only works on Mary Sues.