The group continue on their way and notice people digging for fossils in Grandpa Canyon. Gary shows up for this too. Ash wants to dig for fossils so that he can find a better fossil than Gary.
Gary finds a fossil and an archaeologist examines it. Gary thinks it's the brain of an extinct Pokémon but the professor says it's a Pokémon coprolite fossil (fossilized Pokémon manure).
Meanwhile, Team Rocket plants bombs in the canyon so they can find fossils quicker. Ash notices this just as Meowth lights the fuse. Ash and Squirtle chase it trying to put out the fuse. It gets to the end and Pikachu shoots an electric beam at it in panic. The blast goes off and Ash, Team Rocket, and Pikachu find themselves underground. Squirtle is the only one who escapes quickly enough. Misty and Brock hear the explosion and they run over to it and they find Squirtle. Misty, Brock, and Squirtle quickly start digging to find Ash and Team Rocket.
Meanwhile, Ash and Team Rocket try to find a way out. They meet some ancient Pokémon who they thought to be extinct. Jessie and James say that the blast must have woken up Pokémon that have been sleeping for 1,000 years.The ancient Pokémon are mad at Ash and Team Rocket for waking them up, so they attack but suddenly run off. They are happy the Pokémon left but then they realize why they left: an Aerodactyl appears, grabs Ash, and swoops up into the air .
Meanwhile, Geodude has finally found a hole leading into the cave. A crowd has come to help dig for Ash and Team Rocket. Suddenly, the Aerodactyl flies up out of the hole with Ash in its mouth. Charmeleon wants to battle Aerodactyl and save Ash, but unfortunately Aerodactyl refuses. Upset, Charmeleon evolves into Charizard and chases after the Fossil Pokémon. Charizard apologize to Ash when he used Flamethrower because of side-effect problem.
Misty sees Jigglypuff and asks it to sing so Aerodactyl will fall asleep and drop Ash Jigglypuff happily starts singing. Aerodactyl falls asleep and drops Ash. Ash is caught by Charizard who managed to stay awake. Officer Jenny tells everyone that it was just a dream caused by Jigglypuff’s song and sends the people on their way. Ash gets an egg from the site, which Brock steals from him to take care of.
- Each of Gary's cheerleaders had the letters A-F written on their faces while they were asleep.
- Gary found an example of a Pokémon Coprolite fossil.
- The "Who's that Pokémon?" in this episode is Kabutops.
- This episode shows the first carnivorous pokemon and the first time a pokemon has actually tried to eat a human.