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I'm going to post one I've never seen anyone else bring up: The R.E. League, from a website called Reality's End. The R.E. League is (was) a web-based game created using JavaScript and Perl. People could host Gyms on their websites, which could also have all kinds of special events and stories. The lore for the R.E. League was basically "after the end" nonsense, and like 90% of the stories on each Gym's website were edgelord mary sue fanfiction, but it was still a pretty fun time. I vividly recall one where the Leader called himself "Silver Ketchum," the super special awesome son of Ash Ketchum and (I think) Misty, and the Gym's story was basically you sucking this self-insert's dick and being buddy-buddy with him while a guy named Harlem(?) Hell leading "Team Hell" tried to murder the both of you, even using a helicopter with guns. He dies by falling and splatting on pavement. The vast majority of Gyms are no longer available, as they were hosted on Geocities.