Musashi serves in the Team Rocket trio with Kojiro and Nyarth. She joins a scheme to intercept trainers bound for New Island by disguising herself and her teammates as boat captains aboard a Lapras-shaped sailboat at Old Shore Wharf. This ruse allows them to ferry the protagonist group across the stormy seas deliberately created to block travelers.

When their vessel founders in the violent storm, Musashi and her companions survive and independently reach New Island. They covertly infiltrate the island's inner sanctum, unintentionally trailed by the mythical Pokémon Mew. Inside, they discover cloning facilities where captured Pokémon are duplicated, including Nyarth.

Following the climactic conflict involving Mewtwo and Mew, time reverses and memories vanish. Musashi and her teammates find themselves stranded on New Island with no memory of their arrival. Despite their situation, they appear content and enjoy their time on the island.