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I remember a neat fanfic called Poké Wars which was/is still written by a guy named Cornova.
Basically, Ho-Oh got fed up with mankind's shit and collectively disabled an area in Pokemon brains that dampened their moves' power. The result? Each Pokemon becomes a potential WMD. He also orders them to destroy humans and their "traitor" Pokemon friends, leading to the end of civilization as we know it.
It's very grimdark, with main characters being killed by irate hordes, cities being reduced to rubble by a single Legendary and lots of survivalist drama ("muh broken dreams" and "muh dead family"). Each arc focuses on a group of characters, with main arcs featuring Ash, Pikachu, Brock and Dawn, eventually bringing along many more characters while some side arcs show Ho-Oh's determination while the Legendaries fall into civil war due to his own actions.
Concept and story are 10/10, but it could have better writing, especially when you consider anyone can contribute to the expanded universe, as long as you follow the current events (which characters are dead, how ruined each town is) and check on the author's list how aggressive each species became when it was undampened.
Pic related: becomes a stone cold killing machine
