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nemesis is so funny conceptually. the ultimate bio-weapon. an undefeatable hunter. millions of dollars of research from the most evil corporation on earth. its target? a specific division of a single local midwestern police department

Has there ever been a case of "monster as biological weapon" plot point in any work of fiction that *hasn't* been incredibly stupid?

I don't think I can agree with that one, because if Pokemon Red & Blue was even remotely serious about its themes (especially "trainers and Pokemon working in harmony"), then it wouldn't just let you catch Mewtwo at the end like you would any other Pokemon.

genuine question do r/g/b actually have any themes about humans and pokemon being in harmony? other than the one moment oak tells your rival that he lost because he doesn't love pokemon

That one is a staple of the whole franchise really, but it's definitely the most phoned-in in gen 1 for obvious reasons (such as what you point out here).

There's that build up about how Mewtwo destroyed the lab he was created in a rampage, and one of the chief scientists responsible for it regretted it so much that he dedicated the rest of his life to running an orphanage. But then Mewtwo himself just succumbs to your Pokeball like the rest of them.

Kinda felt like he should have just never been possible to catch.