Our heroes arrive at the Ruins of Alph, the site of prehistoric Pokémon fossils and ancient mysteries. As they look around, Ash notices the remains of an Aerodactyl in the dirt. Suddenly, Professor Oak approaches from behind, telling him that an Aerodactyl fossil is distinguishable by the arrow-shaped tip on its tail. The gang turns around to say hi to Oak, always happy to see him.
Continuing to walk down the trench, Oak converses with Ash, hoping that he didn't get his friends too far out of the way. Brock reminds Oak that the message he left for them mentioned something he wanted to show them. Oak replies that one of his old students has recently phoned him to inform him of an incredible discovery he just made, and that's what he wants to show them first hand.
Inside the laboratory, Oak and his student, Foster, are getting reacquainted with each other. Noticing Ash and the others, Foster drags Oak to the side to tell him that with our heroes, word might leak out of his findings and the media would be swarming the place. Oak reassures that the gang won't say a word, and after giving it some thought, Foster agrees to take them along.
As Ash is watching one of the scientists wash a small fossil with a light water jet, the water stops spraying. Distressed, Foster mentions that this has been happening repeated times in the past, and that a steady water resource is essential to their research. Oak inquires what the source of the water is, and Foster tells him everything comes from a natural reservoir deep in the woods.
At the reservoir, Jessie, James, and Meowth are pumping the water and bottling it for their own profit. Jessie begins to imagine what she could buy with the money they'd make: gowns, gold, diamonds, and anything thing else that's tasteful. James and Meowth have a similar fantasy, dreaming over an abundant supply of food. Suddenly, the pump begins to clog, and Jessie tells James to go and fix it.
Back at the lab, Foster takes the group for a tour, showing them rare fossils, including a Kabutops that may be 10 or 20 thousand years older than the oldest one ever recorded. Oak brings up the subject of one of Foster's theses, which is the aquatic origin of all Pokémon. Foster explains that he believes all Pokémon come from the sea, as the oldest Pokémon fossils have been found under the ocean. This grabs Misty's attention, and she starts to elaborate over how much she loves Water Pokémon, suggesting that she should be Foster's assistant. This time, Brock pulls Misty away by the ear, telling her to dry up.
Foster reaches The Ancient Pokémon Study Park, an interactive, historical environment that recreates the prehistoric world of Pokémon. At a small pond, Ash notices the glowing lichen that's growing on the rocks, and asks Foster when his big surprise is going to be revealed. Foster decides to show them now as a group Omanyte and Omastar submerge from the lake. Realizing that the Omanyte and Omastar are real, everyone is left shocked. Oak kneels down and remembers how it was Omanyte that first sparked his interest in the field of Pokémon Research. He then asks how Foster found such a Pokémon, and he explains that they, in fact, found him, suggesting that maybe their old habitat was destroyed and they accepted the artificial pond as their new home. Brock notes that if word got out of this marvel, it could be a disaster for the Omanyte and Omastar. Foster agrees, and tells that that's the reason he called Professor Oak over: for advice.
Still working on the pump, James finds an Omanyte stuck in the line. Jessie tells him to throw it back in, but he tells her the real value of such an extinct and rare Pokémon. Meowth comes up with the idea of giving a few to the boss, making him happy, and selling the rest on their own, making themselves happy.
Now in the control room, Foster mentions that the cameras mounted around the area were first used for surveillance, but now with them they can view the Omanyte and Omastar without disturbing their habitat. Suddenly, more Omanyte and Omastar begin to appear on-screen, as one of the men rushes in to inform that the water stream is completely gone. Noticing something fishy is going on, Foster, Oak, Ash, Misty, and Brock set out for the reservoir. Outside, Ash sends out Noctowl to take a look at what's going on. It flies over to the reservoir, seeing Team Rocket suck up the Omanyte and Omastar in their tank. Noctowl then returns to the gang, who is having a rough time driving along the dirt path in their jeep.
As Jessie, James, and Meowth are loading the Omanyte and Omastar into their balloon, our heroes arrive. Ash demands for their release, but of course Team Rocket refuses, explaining how they accidentally stumbled over Omanyte as they were pumping water for their bottling business. Oak now realizes the cause of the Omanyte and Omastar's appearance, and that's only because their habitat was being disturbed.
Jessie and James call out Arbok and Weezing respectively, and Ash uses Pikachu, who dodges Arbok's Poison Sting and Weezing's Sludge attacks, retaliating with Thunderbolt, then a Tackle. Team Rocket is knocked back into their tank, blowing it up and returning the water back to the reservoir. Jessie figures they could still make their getaway with the Omanyte and Omastar, so they make their way to their balloon and begin to take off. As Ash is about to have Pikachu attack again, Misty stops him, reminding him that he'd shock the Omanyte and Omastar too. All seems hopeless, when suddenly the balloon stops ascending due to the excessive weight of the Omanyte and Omastar. Meowth realizes this and proceeds to toss a few overboard, but Jessie stops him from doing so. The two get into an argument while Ash sends out Noctowl to peck a hole into the balloon. Team Rocket crashes back to earth, and Pikachu shocks them. Omanyte and Omastar approach, finishing them off with the combined force of several Water Guns.
As the Omanyte and Omastar disappear back to their natural habitat under the reservoir, Oak concludes that it's best to let them go, telling them no living thing deserves to live life as a specimen. Saying their goodbyes, the gang leaves Oak and Foster behind as they continue on their trek to Ecruteak City.