Fergus was one of the Pokémon Trainers who were able to make it through Mewtwo's storm and reach New Island, along with Ash, his friends, Neesha, and Corey. He got there using his Gyarados. When Mewtwo revealed itself to be the one who invited all of the Trainers to New Island, Fergus was the first to speak out against it, claiming that a Pokémon could not be a Trainer. He tried using his Gyarados to battle Mewtwo, but the Genetic Pokémon easily defeated it.
Fergus watched from the sidelines as the original and cloned Pokémon fought endlessly while Mewtwo fought Mew. Ash eventually intervened and was caught in the crossfire, leading Mewtwo to have a revelation and end the challenge. As a result, Mewtwo wiped everyone's memories, including those of Fergus, regarding the events on New Island, and then returned them and their Pokémon to Old Shore Wharf. Later, Fergus joined Officer Jenny and the other Trainers on the pier to watch the storm miraculously clear up.
Fergus presents himself as a tough individual and is often seen with his arms crossed over. He deeply cares for his Pokémon, most of which are Water-types, and is particularly proud of his tamed Gyarados, which serves as a testament to his skill as Gyarados are normally very difficult to tame and thus train. He entered the pool to comfort his Gyarados after it was left injured following a confrontation with Mewtwo.