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You probably want to use a series of flags and checkflags within your script. Flag 0x828 is the flag that allows players to access their Pokemon menu, in your case I would use it at the start of your script to make sure that the player can't just pick a second Pokemon after they receive their first. Flags such as these vary from Rom to Rom, there's a list of them online if you look for them. 0x828 is a FireRed flag btw.
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