Crystal sent some of her Pokémon, including Alakazam, to Emerald who used them in the Battle Pyramid. Emerald used Alakazam to run away from the wild Pokémon that appeared in the Battle Pyramid by using Teleport.
Emerald later also used Alakazam in the Battle Dome against Dome Ace Tucker and his Charizard. Alakazam used Thunder Punch on Charizard which injured Charizard badly. Charizard however used Earthquake to attack Alakazam which defeated Alakazam in the process.