Shelly made an appearance in The Cavern. She is first seen at the Seafloor Cavern, trying to prevent Archie from using the Blue Orb on Kyogre. She explained that her research at the Weather Institute during Team Aqua's takeover led her to discover that Kyogre's power would only destroy the world, instead of improve it. She was, however, unable to stop Archie. She was last seen on board the Submarine Explorer 1 with Archie, being attacked by Primal Kyogre.