Fergus was one of the only Pokémon Trainers who was able to make it through Mewtwo's storm and reach New Island, along with Ash, his friends, Neesha and Corey. When Mewtwo revealed himself to be the one who invited all the Trainers to New Island, Fergus was the first to speak out against it, claiming a Pokémon could not be a Trainer. He tried using his Gyarados to battle Mewtwo, but the Psychic Pokémon easily defeated it.

Just like those of the other Trainers on New Island, all of his Pokémon were cloned by Mewtwo.

(Source:Bulbapedia)