Ash, Misty and Tracey are ridding Lapras to another tropical adventure. Blue sky , warm sea another lovely day in the Orange Islands. Everybody is enjoying themselves. Tracey says that because the ocean is so warm today that they will see lots of water Pokémon out and about. Suddenly a motor boat rushes by swamping Lapras. They see an island in the distance and figure that the boat is headed there. They decide to follow them.
Lapras lands on the beach and Ash and friends get off. Ash thanks Lapras for the ride and it returns to its Pokéball. They find a reporter on the beach talk into a camera about the Legend of Kabuto and the archaeological team that is going on the search to find this extinct Pokémon's fossilized remains. Ash says that they should follow them and see what is happening. The reporter goes to the Base Camp of the archaeologists and starts recording more about a Kabuto fossil that was found on the coast. This fossil is said to have been dislodged from its resting place on the island and is a major find for mankind. Ash takes out his Pokédex in order to get more information about this mysterious Pokémon.
The reporter is still talking about the fossil find and says that she will now talk to the director of the archaeological team. She asks if she can talk to her and the director steps out of the tent. It is Nurse Joy! Ash, Misty and Tracey are surprised. Nurse Joy says that Kabuto are extinct and it is believed that the oil that is in their shells makes a good medicine and may even make people live forever! She continues saying that she doesn't believe this is true but the oil could be a medical breakthrough.
Ash and Tracey walk up to Nurse Joy and say that they want to volunteer themselves to help with the expedition. They then talk into the camera. Ash says "Professor Oak I am going to bring you back a Kabuto fossil." Tracey says "Hey Professor Oak, remember me? I'm Tracey." Misty then comes up to them and starts yelling saying that they are embarrassing her and themselves. We see Team Rocket in their Magikarp submarine looking for Pikachu. James says that if they don't find it the could always look for somewhere to eat.
Back at the campsite everyone is starting to go off on the long expedition to find Kabuto fossils. The Reporter gives everyone a run down on what is happening. Ash yells out "Kabuto watch out!" There are some Pokémon helping on the expedition. Two Machoke are carrying packs, also two Growlithe are sniffing out where the fossil came form and there is a Rhydon who is there to help with the excavation. Team Rocket are walking on a path below the big expedition. James has a big heavy pack and is complaining about it. Up above the Growlithe growl at a big boulder. Nurse Joy says that it is only a boulder and keeps walking. Suddenly the boulder starts to roll down. We see the dark shape of the man who pushed it. Everyone is running back down the track. Ash yells to Nurse Joy to use the Machoke to stop the boulder. She does and t is thrown over the ledge. The boulder ends up going over and hitting Team Rocket. The Reporter is going on about what a miracle that has happened. Pikachu acts like it has seen something. Ash has a look around but sees nothing. They all reach a hidden bay and the Reporter yet again gives a run down on what is happening.
Everyone has gone down to the bay and found a flat area of ground. They are all digging. Ash says that he never knew digging was so hard, but it is all worth it at the end. Tracey says that they have to examine every rock. We see the Machoke and Rhydon working hard digging. Suddenly boulders run the down the hill from all sides. Nurse Joy says to run for it. The Reporter is standing still talking about how the boulders are falling all around them. Nurse Joy then tells Rhydon to Horn Drill one of the boulders that is coming straight at them. After this all of the boulders have stopped. The Reporter talks again about the miracle that has just happened. Misty is scared that a Hit Man is after them. Suddenly Pikachu hears something and runs off chasing it. Ash runs after Pikachu yelling out to it to stop. He sees a shadow up ahead and joins the chase. He finally catches up and tackles the man after a long run. He finds out that he is the guy that has been rolling boulders at them. Ash asks him what does he want with them and the man replies that they have to leave the island! Everyone else form the digging site arrive. They get angry at the man. Nurse Joy asks him why he rolled the boulder at them. The man says he was protecting them. He wanted to scare them off the island before something bad happened. Misty starts yelling at him. The reporter yet again talks into her microphone about the strange, old, decrepit man. The man takes the microphone to tell his story to the world. He tells of a prophecy that goes: When the scavenges come the moon will glow an angry red the land itself will vanish and be swallowed by the sea. Nurse Joy says that they are not invaders they are just there to look for Kabuto fossils. The man says get off the island. Misty says that he is disturbing the island
Suddenly one of the diggers runs up and says that they have found a Kabuto fossil. Everyone rushes off to the digging site including the man. They have a look in a cave and see the Kabuto fossil. Tracey starts to look around for more and discovers that the whole cave is made of Kabuto fossils. The Reporter talks about this amazing discovery and says that her ratings are going to go through the roof. A diggers calls out to another one to go get Rhydon to start digging. The man says no.
There is a big explosion and smoke everywhere. It is Team Rocket. They say their motto. The Reporter says that a disaster is happening. Meowth says that they could use all the Kabuto fossils they get for doorstops in the Boss' mansion. The man says no an recites the prophecy. Team Rocket laugh at him. They light a bomb and throw it to the man. He passes it on until it gets to Ash who throws it away next to a wall. The bomb explodes and Team Rocket escape with all the fossils. As they lift off the toast their first success. Meowth says that even the red moon won't stop them.
As the red moonlight shines through the roof of the cave the mysterious Kabuto fossils began to move. Everyone is scared. The Kabuto become fully alive. Nurse Joy says that this is impossible. The Reporter loses her camera and the Kabuto crawl all over it. The man yells out to run for it. The Kabuto are attacking Team Rocket as well and pop their balloon to send them blasting off again.
Everyone is out of the cave and Nurse Joy says to the workers that they have to leave. The workers ask why and then see the approaching Kabuto. The Kabuto start to jump into the water and swim off. The island is now rumbling and they realize that the island was built around the Kabuto fossils. They start to run for the boat but it is too far away. The man says to run to the forest because that is what the prophecy says. They go to the forest and start making a raft. Rhydon and the Machokes are cutting down trees while everyone else is tying them together. The sea comes rolling in when the raft is almost finished.
The island is rumbling and starting to sink. Everyone gets onto the raft and Ash and Misty send out their water Pokémon (Squirtle, Lapras, Staryu and Goldeen). Ash throws some ropes around their necks and tells them to pull the raft out to sea. As they are leaving trees are falling everywhere and they crash through one. They finally get to the open sea and watch the last of the island fall into the water. They all recite a part of the prophecy. Tracey says that the Kabuto must have lain dormant until the light of the red moon awakened them. Nurse Joy says that Kabuto oil really does keep the Kabuto alive forever. She then says that the world must not know about the secret of the Kabuto. Everyone agrees with her. They watch the Kabuto swim off in the distance going to find a new resting place until the light of the next red moon awakens them.