Ash and Goh have Fossil Pokémon on their mind and Chloe has a science project, so it’s off to the Pewter Museum of Science! There, they meet a man who bears an uncanny resemblance to the excavation leader our heroes met in Unova. But he insists he’s the Museum of Science curator!
Exploring the fossil dig, our heroes find all sorts of ancient artifacts—even a piece of Old Amber!
But Team Rocket is up to its old tricks. When they secretly try to operate a Fossil Pokémon Restorer Machine, it explodes!
Meanwhile, Goh has his eye on a feisty Aerodactyl. After some fierce battling, Goh gently asks if they can become friends. Aerodactyl agrees, and Goh winds up with a brand-new, ancient Pokémon friend!
Ash and Goh set their sights on visiting the Pewter Museum of Science after watching a promotional video for a special exhibit of a giant Shieldon. Professor Cerise suggests his daughter Chloe go along to complete a passion project for her school. Before she can say no, Ash and Goh drag her with them. At the Pewter Museum of Science, the boys are thrilled by all of the revived Fossil Pokémon while Chloe is overwhelmed by the experience. Ash and Goh turn their attentions to the real attraction, the Shieldon exhibition, but are left disappointed by the long queue and when the exhibit suddenly closes for the day. A museum attendant calls out that a fossil excavation is happening, where anyone can get the chance to keep any of their fossilized finds as a souvenir. Goh decides to give it a go, mainly for the chance to get himself a Fossil Pokémon.
At the dig site, Team Rocket are trying to locate a Fossil to restore. Jessie carefully breaks open a boulder in the hopes of finding a Fossil, but is disappointed to see nothing inside. They quickly shift focus when the twerps arrive on the scene. The enthusiastic Curator, who bears a striking resemblance to the leader from the Colossus Ruins, introduces himself as the President of the Pewter Museum. The Curator spies Ash's fossil, and reveals that it a fossilized footprint. He then shows them a Claw Fossil and reveals that such prime examples can be restored using a special machine. Hearing this, Ash and his friends decide to search for fossils, while Team Rocket plot to steal any newly restored Fossil Pokémon for themselves. Goh calls out his Golurk, Raboot and Sobble to help. Chloe soon discovers a fossilized shell, and while not a new discovery, it proves a good research subject for her school assignment. Goh and his team continue searching well into the evening, without yielding any finds. As Chloe and Ash tell Goh that it is time to leave, Goh spots something glistening in the rock wall and recovers it. Taking the find to the Curator to assess, Goh learns the he found an incredibly rare Old Amber; hardened tree resin that often holds ancient DNA material. The Curator decides to try restoring the Old Amber overnight, so Ash and his friends decide to spend the night at the local Pokémon Center while they wait.
The Curator closes down the Museum for the night, leaving the Old Amber to undergo the restoration process overnight. Team Rocket sneak through the ventilation system to steal the Fossil. Jessie, however, become impatient, so James meddles with the restoration machine to quicken the process. The sudden explosion booms through Pewter City, waking Ash and the others up and alerting them to something having gone amiss at the Museum. There, the Curator reveals that the restoration machine has been destroyed and oddly the Old Amber has been restored in record time. The newly revived Pokémon flies overhead and escapes into the distance, with Goh leading the pursuit after it. During the search, Pikachu soon detects something hiding in some bushes, revealing the thieves, none other than Team Rocket. With a new opportunity to catch Pikachu, Jessie and James summon the Rocket Prize Master, with Jessie and James receiving a Nidorino and a Graveler respectively. Ash decides to handle Team Rocket by himself and orders Chloe find Goh.
The mysterious Pokémon settles on a tree branch, allowing Goh to scan it with his Rotom Phone to reveal that it is an Aerodactyl. Goh orders Aerodactyl listen to him, but it goes on the attack instead. Raboot tries a Double Kick counter, but it is knocked down by a Rock Slide. Goh calls out his Golurk, leading Aerodactyl to attack the titan with its wings. Golurk retaliates with a Flash Cannon, which Aerodactyl evades. A second Flash Cannon is countered by Dragon Breath, before Aerodactyl lands a direct hit with an Iron Head. Golurk manages to shield itself as Aerodactyl launches another Dragon Breath. Chloe rushes over to Goh, informing him that Ash needs help handling Team Rocket. Goh replies that he is too busy battling with Aerodactyl.
Meanwhile, Pikachu flees as Nidorino uses Poison Sting and Graveler rolls into a Tackle. Pikachu launches an Electroweb across two trees, leaping through the gaps. Graveler, meanwhile, ricochets off the Electroweb and bowls into the rest of Team Rocket, sending them blasting off. Elsewhere, Goh and Golurk are still trying to wear Aerodactyl out. It is soon struck down by a Hammer Arm and Flash Cannon, and plummets to the ground. Goh rushes to check on Aerodactyl. He empathizes with Aerodactyl, knowing it must have felt scared awakening in an unfamiliar world before reaching out to pat its snout. Goh suggests that it takes its time adjusting to the new era by joining him, and Aerodactyl quickly calms down. Having earned Aerodactyl's trust, Goh catches the Fossil Pokémon. He calls out his new partner, who happily flies around him. When Ash and Goh later report the results of their museum trip to Professor Cerise and express how much fun they had, they're surprised to hear Chloe also saying that she had fun.