Continuing to recover from his Oreburgh City Gym battle loss, Ash gets in plenty of training with Turtwig, Pikachu and Aipom. Dawn tries to convince Ash to send home for Pokémon that are strong against Rock Types, but Ash is persistent on using the ones he currently has. Brock lends Ash Sudowoodo to train against, as its Rock Head Ability is immune to such moves as Double Edge.
Back at the Pokémon Center, Dawn finds out that the next Pokémon Contest is at Floaroma Town, where she intends on heading next. Team Rocket steal the Fossil Restorer, unaware that a Pokémon is still inside. Out pops an Aerodactyl, which refuses to be caught by Jessie. Dawn finds Aerodactyl when it attacks the citizens of Oreburgh City; in the ruckus, Kabuto and Armaldo get free as well!
Roark, Brock and Ash triple team the Ancient Pokémon, but Team Rocket show up to steal them all. When Kabuto and Armaldo return to their Poké Balls, Dawn's Piplup and Buneary use their agility and grace to avoid Aerodactyl's Giga Impact, allowing Dr. Kenzo to get it back into its Poké Ball! Roark's newly evolved Rampardos finishes off Team Rocket's robot and blasts them off, putting everything back as it should be. Ash asks Roark if he can take on Rampardos in their rematch and he agrees, giving Ash time to craft a battle strategy!
After Ash's Oreburgh Gym defeat, he is not letting the loss put him down as he trains with his Pokémon for a rematch. While Pikachu, Aipom, and Turtwig’s attacks are impressive, smashing through coal ore pillars with ease, Dawn brings up the type disadvantage his team (save for Turtwig) faces against Roark's Rock Pokémon. Though Ash refuses to retrieve his other Pokémon from Professor Oak or borrow Dawn's Piplup for the match. He remarks that Paul won with type disadvantages and knows that he can do the same, which settles the difference. However he does take up Brock’s offer, deciding to practice against Sudowoodo since it resembles Roark's Pokémon by type and the Rock Head Ability. Dawn is also inspired and decides to head back to the Pokémon Center to practice new combinations. When she does get back, the TV inside shows Marian announcing the location of the next Pokémon Contest, which is in Floaroma Town.
Dr. Kenzo and his scientists at the Oreburgh Mining Museum soon discover that one of the three Fossil revival machines was stolen, immediately reporting it to Officer Jenny. None of the revived Pokémon were affected, but one points out that the stolen machine had a Fossil inside, which was in the process of being revived. The culprits, Team Rocket celebrates the successful theft of the machine. They decide to revive Fossils, but they realize that none of them grabbed any Fossils during the heist, which sparks an argument. The revival machine suddenly activates, cutting off the argument, one of the screens displaying complete rebirth. The doors open, and smoke pours out as the figure inside awakens, revealed to be an Aerodactyl. Jessie tosses a Poké Ball to catch it, but Aerodactyl merely swats it away. It flies off and initiates Giga Impact. While James tries to use information cards to figure out what the attack is, Aerodactyl swoops down and attacks Team Rocket before it flies towards Oreburgh City.
Ash is still training hard with Brock, pitting Turtwig against Sudowoodo. Ash is trying to find the strategy he needs to win, reflecting on his loss on how Roark's Pokémon were fast as well as being able to negate pure power attacks. Roark comes by, intent on digging for more Fossils, and praises Ash’s effort. When he finds a Fossil on the ground, he reveals to Ash and Brock on how he met his Cranidos, being the first Fossil to be revived via the machine.
Dawn is training with her Pokémon when Aerodactyl appears, firing Hyper Beam at random. She quickly shields her Pokémon, avoiding the blast, before checking her Pokédex to confirm the Flying creature’s identity. Aerodactyl continues to rampage across town, firing Hyper Beam at random locations, making its way to the museum. It destroys part of the structure, releasing a revived Armaldo and Kabutops. The scientists rush out to try and contain the Pokémon, but Aerodactyl fires a Hyper Beam to stop them. Armaldo and Kabutops attack Aerodactyl with Hyper Beam and Mud Shot, but it flies off, leaving Armaldo and Kabutops to roam freely.
Ian rushes back to Roark and alerts him to the situation. Officer Jenny quickly orders all citizens to evacuate. Officer Jenny and the scientists corner Armaldo and Kabutops at the Oreburgh Mine. Roark steps in and sends out Cranidos to distract them with Flamethrower. Pikachu and Sudowoodo attempt to get close, but Armaldo and Kabutops stop them with fierce attacks. Cranidos uses Zen Headbutt, which freezes both Pokémon. However, Team Rocket shows up and grabs all three Fossil Pokémon with their revival machine mecha.
Pikachu prepares to attack, but Roark reminds them that the Fossil Pokémon and the revival machine are both at risk. Aerodactyl shows up and fires a Hyper Beam, freeing all three Pokémon and knocking down the machine. Dr. Keno and his assistant quickly recall the Armaldo and Kabutops as Aerodactyl launches Giga Impact at Cranidos. Cranidos stops the attack at first, but it gets pushed back into the group, sending them all rolling. Aerodactyl fires Hyper Beam at Ash and Pikachu, but Dawn arrives, her Buneary and Piplup stopping the attack with Ice Beam and Bubble Beam respectively. Dawn steps forward as Aerodactyl initiates another Giga Impact. Buneary and Piplup wait until it gets close before jumping and spinning past the attack with ease, with the evasive technique impressing Ash. The pair jump and knock down Aerodactyl before Dr. Kenzo throws a Poké Ball, catching it.
Team Rocket uprights the mecha, though Roark confronts them. As they try to run, Cranidos pursues, but Meowth fires a net missile to imprison Cranidos. Cranidos begins glowing, evolving into Rampardos and shattering the net. Rampardos charges forward and easily catches up, grabbing the machine and detaching the revival machine before using Zen Headbutt to destroy the mecha and send Team Rocket flying. Dr. Kenzo is grateful to have the Fossil restorer back, while and Officer Jenny salutes Rampardos for its help. Afterwards, Ash asks Roark for the rematch the next day, which is accepted. Ash then asks Dawn to help him with training for the battle, which she accepts since it’ll be good practice for her as well.