After you beat Trainer Red, champion of Kanto, go to Saffron City and in the giant building. Then talk to Steven from Hoenn. He'll give you choice of 3 stones. Choose green 4 Treecko, blue 4 Mudkip, or red 4 Torchic. I think.
How Do I Get Treecko In Soul Silver?
After beating Red at Mt. Silver, you need to go to Silph Co in Saffron City. Steven Stone should be standing by the reception desk. Talk to him with and empty spot in your party. Whenever he asks you what color stone you would choose, Red is for a Torchic, Green is for a Treecko, and Blue is for a Mudkip.