Once you defeat the Elite 4 and the Champion and manage to gather all 16 badges (both johto and kanto) you will be able to go to Mt.Silver (after talking to prof.Oak). At the peek there is a trainer known as Red, once you beat him go to prof Oak and he will ask you to to chosse one of these 3 pokemon: Bulbasaur, Charmander, Squirtle. You can also find Steven in Silph Co. where he will ask you to choose a color: Green~Treecko, Red~Torchic, Blue~Mudkip.
Hope this helped!
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