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I owned Yellow but truthfully I have no idea what I used the Masterball on, maybe something boring like Mewtwo.
But my first real stand out encounter was Gen 2.
>south of Goldenrod just trying to fight some Pokemon to help raise some of the babies I was hatching
>Suicune appears
>HOLY SHIT WHAT THE FUCK IS THIS THING WHAT IS THIS
>just toss my Masterball at it and got it
Mind you, I did that tower thing but I had no idea the Legendary Dogs roamed Johto, so that caught me off guard.