Professor Oak and Tracey are visiting the island where Gary is currently doing research. But not only are Butch and Cassidy tracking their movements, the Professor and Tracey encounter a raging Aerodactyl the minute they arrive on the island! The researchers on the island study ancient fossils, and Gary had the idea to use a piece of amber and a fossilized Egg to revive ancient Pokémon. However, as soon as they revived Aerodactyl from the Egg, it escaped and went on a rampage! Crystal, the little sister of head researcher Dara, asks all her Pokémon friends on the island to help look for Aerodactyl. Sure enough, one of the Farfetch'd sees Aerodactyl and leads everyone to the spot.

Aerodactyl is sleeping near the spot where the fossilized Egg was found, but it wakes up and flies off. Tracey tries to grab onto it, only managing to jump off after a wild ride. Then, before everyone's eyes, Butch and Cassidy snag Aerodactyl in a net—Team Rocket has come to the island to grab this ancient Pokémon! Gary's Umbreon and Crystal's Ivysaur are able to beat Team Rocket, but Aerodactyl frees itself and flies away, agitated. It seems overwhelmed by its new environment, so the researchers figure out what food it likes in the hopes of understanding Aerodactyl's behavior.

As predicted, they find Aerodactyl eating in a grove of fruit trees, only to have Butch and Cassidy show up yet again. This time, they use a helicopter to help capture Aerodactyl and carry it away. Crystal's Ivysaur tries to stop them, but Gary just has his Dodrio jump on the helicopter to wreck Team Rocket's plans and help free Aerodactyl. Once free, all Aerodactyl wants is to eat in peace, but Gary approaches it with a peace offering of fruit. That wins Aerodactyl over, and soon Aerodactyl is happily eating the food that Crystal offers, too. With everything on the island back to normal, Professor Oak and Tracey say their fond farewells and return to Pallet Town.