Ash and his friends arrive at the Ruins of Alph, currently an active Fossil dig site, to meet Professor Oak, who shows them around while telling them that he found out about a mysterious discovery. They meet up with Foster, a scientist and one of Oak's top students from Celadon University. He takes Oak aside and tells him that it would be dangerous if any information about the discovery would be leaked, but Oak vouches for the group and their reliability. During the tour Ash notices a man washing a bone; Foster explains that the man is removing the dirt from a Fossil they just found with a special device that uses a powerful but harmless water spray.
After determining the fragment's source, the device stops working, with Foster telling they've been having water flow problems lately. Oak asks about the water's source and Foster answers, specifying it's a natural crystal clear water reservoir deep in the woods. The culprits behind the water shortage are revealed to the troublesome Team Rocket, who hope to get rich by bottling up the spring water. The water pump then stops working. As James tries to repair the pump, he discovers an Omanyte who was jamming the pump. Team Rocket are thrilled by the discovery and immediately start searching for more Omanyte to send the boss. Switching the pump back on, Team Rocket start capturing several Omanyte.
Meanwhile, Foster informs Oak and the kids that his studies have found that the first Pokémon appeared 2,000,000 years ago and all the Pokémon has its origins in the ancient seas. Misty is thrilled to hear the latter, revealing her love for Water-type Pokémon. Then, ironically Brock drags Misty away from Foster by her ear. Later, Foster leads them to a forbidden entry saying it is a place 2,000,000 years in the Pokémon past. As the door opens, a robotic Aerodactyl is flying around. Foster names the place the Ancient Pokémon Study Park; a special interactive and unique environment that recreates the ancient Pokémon world set to be opened to the public next week. They proceed to a lake where a huge statue of a Kabutops is seen preying on a fish. Then, Ash asks him about his mysterious discovery which Oak hinted at earlier. Foster tells them to wait for a moment, before a real Omastar and two Omanyte come out of the water. Initially, they all think the Pokémon are robots but Foster informs them that they're real. When the group reacts to this, the Pokémon frighten up and bury themselves in the sand. After witnessing this, Oak reveals that it was an Omanyte who inspired him to become a Professor. It all goes back when he was 6 years old and along with his class, they visited a Pokémon museum where he saw an Omanyte shell. Foster then reveals that he discovered them after their natural habitat was disturbed so they came to this Park. Ash takes the opportunity to scan the thought-to-be extinct species with his Pokédex. Soon one more Omanyte and Omastar appear, and Foster reveals that the previous ones appeared the same day they had water problems.
The door opens, and another scientist enters informing them the water has stopped flowing completely. They all agree to go to the reservoir. Outside the building Ash sends his Noctowl to scout the reservoir while Foster drives everyone over in a SUV. Noctowl soon returns and Ash realizes there is something is up. Arriving at the reservoir the group sees that Team Rocket have loaded up their hot-air balloon with the Pokémon. The trio recite their motto. Meowth then explains how they found the Pokémon, leading Oak to realize that the Omanyte and Omastar from the Park arrived when Team Rocket started pumping the water. After Foster orders them to return the Pokémon, though Jessie declines and sends her Arbok and James his Weezing to attack. When Pikachu gets sent in to fight, Arbok proceeds to use Poison Sting and Weezing with Sludge, but Pikachu dodges both attacks then uses Thunderbolt followed by a Tackle which sends them into Team Rocket and blowing up the pump. Jessie and James recall their Pokémon back and proceed to lift-off with the nabbed Omanyte and Omastar. Suddenly, the balloon ascent stops due to being overloaded by the heavy Pokémon. Ash sends his Noctowl again and orders it to make a hole in the balloon bringing Team Rocket crashing down. With a Thunderbolt, Pikachu shocks them and the Omanyte and Omastar send Team Rocket blasting off with Water Gun.
The Omastar and Omanyte eagerly return to the water. Foster is pleased to see the ancient Pokémon returning to their true home, while Professor Oak is tempted by the chance to study them, he remarks that it is best they be left in peace. The Omanyte and Omastar burrow deep into the lakebed, reaching a hidden underwater cavern full of more Omanyte and Omastar. Afterwards, Foster and Professor Oak bid farewell to Ash's group.