Instructions
Beat the Final Four, then load up your finished game. Go to the SS Tidal and speak to Scott, who will open the option to go to the Battle Frontier.
Speak to the lady on the SS Tidal to head to the Battle Frontier. Once you land, head into the Battle Tower, go past the Battle Dome, and take a right.
Access the PC and deposit the Pokemon in your party you wish to clone. Exit the PC menu and save your game.
Access the PC again and take out the Pokemon you've recently deposited. Afterwards, head to the far right of the Battle Tower to speak with the Wireless Attendant.
Choose "Open-Level Battle" as the battle type and select two Pokemon you do not wish to clone, to fight in the Battle Tower. When you are informed that your progress must be saved, select "Yes."
Wait until the Attendant confirms again to save your game. Turn off your Game Boy Advance, then turn it back on and reload your game. Check your PC to ensure that the Pokemon you deposited earlier in your PC are the same as the ones in your party.