Aboard Lapras, the group follows a news crew to Fukuhara Island No. 4, where a scientific expedition is underway after the discovery of a fossilized Kabuto. While on the island, Ash and his friends are shocked to learn that Nurse Joy is the director of the Kabuto excavation. She tells the new reporter that the excavation hopes to study the habitat of the extinct Pokémon Kabuto. She also remarks that they would like to find out if the claims about Kabuto oil, considered a youth elixir and health medicine, are true or not. After hearing all of this, Ash and Tracey jump in front of the reporter's camera and ask if they can help with the fossil digging. A moment later, Ash looks into the camera and makes a scene, which in turn causes Misty to grab him while yelling at him for embarrassing them.
Meanwhile Team Rocket have been watching the whole scene from their Magikarp submarine, at which Jessie says that she wonders why a television crew would be on the island, which then prompts Meowth into saying that if they hurry up and catch Pikachu, they can then maybe catch some face time too.
Nurse Joy leads a group of explorers, the news crew, and Ash's group to the digging site. A group of Growlithe also accompany the team, while Machoke are seen carrying some equipment and several Rhydon for drilling holes. As they pass by, a mysterious silhouette of a man is seen behind a tree. They eventually reach a small cliff path which Misty is very uneasy about because of the height. At the same time Team Rocket is shown following the same path on a lower section of the cliff. As Nurse Joy's team moves on the Growlithe start to growl at a large boulder on a hill, but Nurse Joy dismisses the alarm. Suddenly the boulder, which is actually pushes, falls and starts racing towards them. While the group runs down the hill, Ash suggests that Nurse Joy use the Machoke's strength. They Pokémon succeed and the team is saved. Unfortunately for Team Rocket, the boulder then rolls off the side of the cliff and knocks James into a canyon.
As the team continues to walk, a silhouette of a man is seen, but this time from behind a rock. Pikachu catches a glimpse and looks over which catches Ash's attention. Ash turns around to check though sees nothing suspicious. Eventually the team reaches their destination, a hidden bay on the island's desolate northern shore. Right away the crew and their Pokémon start to excavate. As Ash, Tracey, Pikachu, and Togepi dig, several boulders start falling onto them. Luckily Nurse Joy commands Rhydon to use Horn Drill, which shatters the crashing boulders and once again the team is saved.
After the second near boulder catastrophe Misty mentions that she thinks that someone is responsible for all of the incidents. Tracey refutes her claims and clarifies that the island is supposed to be deserted. Just as he says that a dark silhouette of a man is seen running from behind a tree at which Pikachu notices and starts chasing after him. Ash follows suit and ends up jumping on the man, bringing them both to the ground. As the rest of the crew catches up, the identity of the man is finally revealed to be Umberto. With that, he then sternly tells them to leave the island and admits he while has been pushing the boulders onto them.
Umberto explains that he was only trying to keep them out of harms way. He then tells of an ancient prophecy which implies that anyone who comes to the island to disturb the Kabuto will cause the island to be swallowed by the sea. At that moment, an explorer comes running into the forest, ecstatic to have found another Kabuto fossil. This then causes the team and the man to venture into a cave where the fossil was found. When they get to the end of the cave they find walls of Kabuto fossils. Team Rocket's arrival causes the cavern walls to crumble. James then throws a bomb that gets passed around until Ash catches it and throws it at the wall of Kabuto Fossils. The fossils then explode off the wall, and Team Rocket wraps them up in a net and tries to get away with their hot air balloon. The Kabuto then end up coming to life as moonlight hits them and one ends up popping Team Rocket's balloon which leads to them blasting away.
It is soon apparent that the Kabuto were Fukuhara Island No. 4's foundations, and the island begins to flood as the fossil Pokémon become more disturbed. As the island starts to collapse the team decides to head for the boat, but Umberto insists that the prophecy said to run into the forest and make a raft. So they listen to him and start building a makeshift raft. As the island sinks they all jump onto the raft, and Ash sends out his Lapras and Squirtle, while Misty sends out her Staryu and Goldeen to help pull the raft. They all make it out to sea and watch the island completely sink. Joy remarks that maybe the Kabuto oil does cause them to live forever. She then apologizes to Umberto for not believing him, and the news reporter says that she thinks it's best that no one ever finds out the Kabuto's secret. At the end, the Kabuto are seen swimming towards the moonlight, looking for a new safe home.
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