Milotic was sent out as Lucy's third Pokémon against Emerald. It used Mirror Coat, as Emerald's Starmie used Psychic, which sent the attack back to Starmie. It was knocked out by Starmie's Thunderbolt, but it too was knocked out.
Later on, Milotic was used as transport for Lucy to get to Artisan Cave with the other Frontier Brains, minus Factory Head Noland, and Emerald. While inside, she was used to battle against dozens of wild Smeargle, along with the other Frontier Brain's Pokémon.
Due to the flood and the rental Pokémon rampaging around the Battle Frontier, Lucy sent Milotic to the battle.