As a kid playing through red the first time I ended up using my master ball on Zapdos because I had no idea what was in the game and didn't know that Mewtwo was a secret super boss. I eventually caught him without the master ball but holy crap was that an ordeal.
"History Is Much Like An Endless Waltz. The Three Beats Of War, Peace And Revolution Continue On Forever." - Gundam Wing: Endless Waltz