Ash and his friends are walking in an area called Grampa Canyon when they see a large group of people walking with picks and shovels. Gary appears and explains that he and the group are here for the Fossil Rush, because of a great 'Pokémon Discovery'. Ash resolves to join in, so as to embarrass Gary by finding a fossil before he does. Jigglypuff also appears, ready to sing, but the group leave without noticing it.
Ash, Misty, and Brock soon find a large area of the canyon where many people, including Gary, are digging. However, they also stumble across Team Rocket, who reveal (accidentally) their plan to blow up the canyon and steal all the fossils. As Meowth lights the fuse, Ash runs up to Team Rocket, and sends out Squirtle in an attempt to put the flame out. Squirtle, Pikachu and Ash chase the fuse, trying to put it out; Jessie, James, and Meowth (along with Arbok and Weezing) try to stop him. Team Rocket then fall and start rolling, resulting on a ball of people and Pokémon rolling into Ash, landing right beside the dynamite. As the fuse draws near to the dynamite, Pikachu panics and uses ThunderShock, causing the dynamite to detonate. Ash, Pikachu, Jessie, James, Meowth, Arbok, and Weezing are now trapped in an underground cave, and only Squirtle escapes from the rubble. Hearing the explosion, Misty and Brock run to the pile of rubble and start digging out rock and soil with Squirtle.
In the cave, Ash, Pikachu, Team Rocket, and their Pokémon begin arguing over whose fault it is that they're down there. The group is soon confronted by Fossil Pokémon that they do not recognize. Ash checks his Pokédex, and the Pokémon are revealed to be Omanyte, Omastar, Kabuto and Kabutops. Jessie and James begin to speculate that the explosion must have awakened them from thousands of years of sleep. Regardless, Team Rocket begin to contemplate stealing the Pokémon for their boss, and attempt to catch them by throwing Poké Balls at the Fossil Pokémon. A Kabutops blocks the balls, and they are rebounded at Meowth. All of the Fossil Pokémon start approaching the group to attack, so Ash sends out his Charmeleon, but it refuses to help. A chase scene ensues, where the Fossil Pokémon are winning the chase. Then, all of a sudden, the Pokémon run away deeper into the cave. Originally confused, the group soon realize why the Pokémon ran off: an Aerodactyl swoops in, knocking over Charmeleon. Angry, Charmeleon tries to attack the Aerodactyl, but is knocked out before it gets a chance. Aerodactyl then grabs onto Ash with its claws, and begins to fly towards the surface. Before the flying Pokémon can get too far, Pikachu and Charmeleon jump on board.
Back above ground, Brock's Geodude had finally dug a hole through the rubble. The Aerodactyl flies out of the hole in the ground, dropping Pikachu and Charmeleon on its way out, and perches on a cliff with Ash still in hand. Charmeleon wants to battle the Aerodactyl as Aerodactyl had earlier annoyed him, but the Aerodactyl just taunts it. The anger this causes Charmeleon seems to make it evolve into Charizard. Ash is happy as he thinks that Charmeleon has evolved to rescue him, but then realizes he merely wants to battle Aerodactyl for his own pride and has no thought of rescuing Ash.
Meanwhile, Misty sees Jigglypuff and tells it to sing to make Aerodactyl fall asleep. Jigglypuff agrees and quite happily sings, of course sending everyone in the canyon to sleep. Aerodactyl, now asleep, falls into the rubble, dropping Ash before falling. However, Charizard manages to stay awake by covering its ears and catches the sleeping Ash before he hits the ground, but falls asleep anyway once landing on the ground. Jigglypuff, seeing everyone has fallen asleep, draws markings all over everyone's faces with its marker out of anger. After awakening, Officer Jenny announces that the whole thing was a dream caused by Jigglypuff's song, although Ash knows it wasn't.
As Ash and the gang leave, Ash reveals that he had found a Pokémon egg at the site, causing the trio to fight playfully about who should get to raise and keep the egg. Brock takes the egg and runs away, promising to "take good care of it", with Ash and Misty in tow. Meanwhile, Team Rocket and their Pokémon are still trapped in the cave, with the sleeping Fossil Pokémon only feet away.