Instructions
Travel to the Battle Tower in the Battle Frontier.
Access the PC in the Battle Tower and place a Pokemon into Box 9. Place a Master Ball in the Box with your Pokemon.
Exit and save your game.
Access the PC once again and take out the Pokemon you just put in.
Approach the woman who handles Link Battles and select "Challenge," followed by "Open Level." Choose the Pokemon you wish to battle with, provided it isn't the one you're cloning.
Choose to save your game when she asks. The game will temporarily freeze during this process.
Turn the Game Boy Advance off and on again or reset the game by pressing "A," "B," "Start" and "Select" at the same time.
Start your game again and access the PC to find a cloned Pokemon as well as a cloned Master Ball.