Fergus was one of a few trainers who managed to make it through Mewtwos storm and reach New Island with Ash, Neesha, Corey, and others. When Mewtwo revealed himself as the one behind inviting all trainers to New Island, Fergus was the first to speak out against him, arguing that a Pokémon could not be a trainer. He attempted to use his Gyarados in battle against Mewtwo, but it was easily defeated by the Psychic Pokémon. All of Fergus's Pokemon were cloned by Mewtwo like those of other trainers on New Island.