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How did Pikachu and Piplup end up stranded on a deserted island? Mere hours before, they were exploring the ferry from Iron Island to Chocovine Town, the site of Dawn's next Contest. Below decks, they ran into Team Rocket who promptly kidnapped the two Pokémon and took off in their Magikarp submarine! Ash and Buizel took to the water in pursuit, but a strong current swept Pikachu and Piplup away. While Officer Jenny helps Ash, Dawn and Brock look for the missing Pokémon, Pikachu and Piplup end up on an island where they must fend for themselves until help arrives!
Pikachu and Piplup try to signal for help, but to no use. Little do they know, this island is located in "Diablo's Ocean|, a place where strange rocks jut out of the sea. In fact, as they explore the island, Pikachu and Piplup see a school of Mantyke bringing pieces of rock upstream to a waterfall where a Corphish stacks the rocks around a glowing jewel! Corphish explains that it all started one stormy night, when something flying over the island was struck by lightning and crashed. When Corphish and Mantyke went to investigate, they found an unusual orb that glows in response to the rocks of Diablo's Ocean. Pikachu and Piplup help Corphish and Mantyke quarry more rocks and are spotted by Staravia and Buizel who are out searching for them.
As the Pokémon drop off their latest cargo of rocks, the jewel glows brightly as if it is about to awaken! But Team Rocket and their Magikarp sub pop up to seize Pikachu and Piplup, only to be stopped by Staravia and Buizel. Right behind them are Ash and his friends on Officer Jenny's speedboat! Before a battle can break out, the jewel transforms into a Deoxys which generates a magnetic force as it taps the rocks--that are in fact meteorites--for energy. Team Rocket tries to grab this Legendary Pokémon, but it easily destroys their submarine, resulting in them blasting off, and saves our heroes from the falling debris. Deoxys then takes off into the sky where an aurora has appeared overhead; maybe Deoxys use the meteorites in Diablo's Ocean to recharge their energy? It's another Sinnoh mystery uncovered as Officer Jenny takes our reunited heroes to Chocovine Town!