Corey was one of the only Trainers to make it to New Island. He made it by flying on the back of his Pidgeot. Along with Neesha, Fergus, and Ash and his friends, Corey witnessed the revelation that Mewtwo was trying to destroy the world.
Corey tried to defeat Mewtwo's clone Venusaur using Bruteroot, his Venusaur; however, Mewtwo's Venusaur easily defeated Bruteroot with a Vine Whip, sending it flying. He also tried using his Rhyhorn against Mewtwo.
Like those of the other Trainers on New Island, all of his Pokemon were cloned by Mewtwo.