While riding around the Orange Islands on his Lapras, Ash finds a message in a bottle from Marissa of Sunburst Island, who is looking for someone who knows about a Pokémon called the Crystal Onix, which Tracey is aware of. Ash and his friends travel to Sunburst Island, where they overhear an argument between a rival shopkeeper and a young girl, and go to intervene. The young girl is revealed to be Marissa. They then meet her older brother, a struggling young shopkeeper named Mateo, who is seeking inspiration from the legendary Crystal Onix. He smashes one of his Pokémon statues out of frustration and complains they are lifeless compared to his grandfather's works. Mateo tells the group that his grandfather once saw the actual Crystal Onix and shows them his grandfather's Crystal Onix statue. Ash and his friends decide to help him in his search.
Team Rocket arrives on Sunburst Island as well, and are in awe of the glass shops. Jessie and James start picking up various pieces and admiring them. Meowth yells at them to knock it off, causing Jessie and James to break the glass items they were holding. The shopkeeper hears this, and tells them about the "You break it, you bought it" rule before he puts them to work, since they don't have the money to pay him back for the items they ruined. While they are chopping and carrying wood, they overhear the shop owner and another employee mocking Mateo for searching for the Crystal Onix. Team Rocket becomes interested and they leave in search of it.
Tracey sends out Venonat to help find the Crystal Onix. Mateo holds up the Crystal Onix statue and Venonat scans the image. The group is led to a series of rocks that are shaped like the body of an Onix. Disappointed, Tracey recalls Venonat and sends out Marill, noting that its large and sensitive ears may prove useful. Tracey plays Marill a recording of Onix's cry and Marill quickly detects something. It leads them to a body of water and points across the water to a small island with a cave. The water begins to part, revealing a land-bridge. However, the group suddenly falls into one of Team Rocket's pitfall traps. After reciting their motto, Team Rocket runs off to find the Crystal Onix. Ash and his friends climb out of the hole and run after them. Once they get to the opening of the cave, they discover Team Rocket, caught in their own traps. Misty refuses to help them and they all enter the cave by themselves.
At the end of the cave, they come across a lake. Marill dives in and then, followed by the Crystal Onix. Mateo calls on his Cloyster, thinking it has the type advantage. However, its Water Gun attacks prove to be useless. The Crystal Onix retaliates and knocks Cloyster out with one headbutt. Just then, Team Rocket shows up, having freed themselves from their traps. Jessie and James send out Arbok and Victreebel in an attempt to catch the Crystal Onix, while Ash and Misty send out Pikachu and Staryu to counterattack. Staryu and Pikachu attack Team Rocket, then the Crystal Onix smacks them into a blastoff.
Seeing as Cloyster's Water attacks proved to be useless against the Crystal Onix, Mateo sends out his Charmeleon. It dodges a Rock Throw and uses Flamethrower, which engulfs the Crystal Onix in flames. Onix glows a brilliant red and Charmeleon fires its Fire Spin* attack. Mateo and the Crystal Onix then stare at each other. At that moment, Mateo sees duplicates of himself in Onix's glass facets. The Onix then faints and falls into the water. Ash calls out for Mateo to catch it, but Mateo says he doesn't need to, since he has found inspiration through the Crystal Onix. It promptly dives back into the water. Back at his shop, Mateo and Charmeleon are busy making a glass figurine while Marissa is happy to see her brother working again. Ash and his friends wave goodbye to Mateo and Marissa, wishing the pair all the best with their glass shop. On their trek to the water, Ash admires Mateo's handcrafted and lifelike glass Pikachu sculpture.