It was operated by Dr. Fuji, a scientist who was forced into working for Giovanni in exchange for research funding. It was here that the artificially-created Pokémon Mewtwo was born, from a fossilized eyebrow of Mew. In its anger at the humans' ideals, Mewtwo destroyed the facility on the island, proceeding to transform it into his base of operations. He then restored the cloning facility, calling on the strongest Pokémon trainers to venture to New Island, in order to clone their Pokémon. After witnessing the lengths Ash would go to protect his Pokémon, Mewtwo saw the error of his ways, and left New Island with the clones. In a post-credits scene, Team Rocket were seen venturing through the abandoned New Island, which in disuse became enveloped in plant life.
In the movie, the distance that the trainers journeyed from Kanto to New Island was shown to be very short. However, this was before the change that saw New Island become positioned between the Sevii Islands and Orange Archipelago respectively.