just like gold or silver
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in Pokemon crystal the best Pokemon to have are feraligator(evolved form of totodile), weepinbell, kadabra, ledian (i would advise you to this Pokemon ice punch and headbutt), and pidgeot. these are the Pokemon i beat the elite four with
at the grass in front of crystal cave. you can get to it, by beating the elite four and get all gym badges in johto and kanto hope that helped
SS Aqua after you have beaten the elite four in the captains room the gentleman gives you it
You can't until you have the S.S.Ticket, which you get after you beat the Elite Four in Kanto.