Ash is busy training his Pokémon for his rematch at the Oreburgh Gym. Dawn and Brock notice that Ash's Pokémon are doing well. Buneary even walks up to Pikachu and tells how great of a job it is doing. Ash says that he will be able to get the badge in no time if the training goes well. Dawn tells Ash that his Pokémon aren't very good match-ups with rock Pokémon. She tells Ash that he should call Professor Oak to send him some of his other Pokémon. Dawn even offers Ash her Piplup for the battle. Ash says that he doesn't need to change Pokémon. No matter who the opponent is, there's always a weakness. Ash states that he is a team with his Pokémon, and they will stay a team. Even Paul didn't have good Pokémon against rock types, but he won anyways. Brock has an idea. He sends out Sudowoodo. Dawn is confused, but Ash understands right away. Sudowoodo has the Rock Head ability, the ability that prevents recoil damage. If Ash can train his Pokémon to beat Sudowoodo, he may have a chance against Roark's Pokémon.

Dawn states that she has a few contest moves that she wants to practice with her Pokémon. She wishes Ash good luck for his gym battle, and then she runs back to the Pokémon Center. When Dawn arrives at the Pokémon Center, she sees Mary, the contest host, on TV. Mary states that there's an upcoming contest in Floroma Town. Dawn definitely doesn't want to miss it.

The fossil researchers have found out that there Pokémon restoration machine has been stolen. They note that none of the Pokémon were taken in the process, but there was a Pokémon in the machine that was in the process of being restored. Team Rocket has stolen the machine. They plan on using the machine to revive many fossils and build an army for Team Rocket. Suddenly, then monitor states that the rebirth if complete. Team Rocket realizes that there was already a fossil in the machine. The door to the machine opens, and an Aerodactyl appears. Jessie throws a Pokéball at Aerodactyl to capture it. Aerodactyl angrily swipes the Pokéball back at Jessie. Then it prepares an attack. Jessie asks James what attack Aerodactyl is doing. Once Team Rocket is attacked by the Aerodactyl, James finds out that it's a Giga Impact attack. Then the Aerodactyl flies towards town. Team Rocket decides to chase after the Aerodactyl. Meowth thinks they should also steal some more fossils while they are in town.

Ash continues training his Pokémon. Turtwig uses Razor Leaf, and Sudowoodo fights back with Double-Edge. Ash notices that Turtwig's moves have gotten a lot stronger. However, rock Pokémon have lots of power and speed in them, and he knows he can train his Pokémon to be better. Brock offers a break because the Pokémon are worn out. Roark notices that Ash is working real hard for his rematch. He tells Ash not to work too hard and to know that he shouldn't get worked up over Paul. Ash thanks Roark for the good advice. Roark goes back to digging again. He states that his Cranidos was restored from a fossil and that Cranidos was the first Pokémon that was used on the restoration machine.

Meanwhile, Dawn is having her Pokémon practice their movesets for the upcoming contest. Suddenly, the Aerodactyl swoops above them and uses its Hyper Beam on the ground. Dawn looks up Aerodactyl in her Pokédex. One person thinks that the Aerodactyl might've come from the museum. The Aerodactyl continues to terrorize the town. It fires rapid Hyper Beams at everyone. Even the museum gets hit leaving a hole in the wall. Kabutops and Armaldo begin to escape the museum. The researchers and Officer Jenny run out to recover Kabutops and Armaldo. Aerodactyl fires a Hyper Beam at them. Then it flies away again, and Kabutops and Armaldo chase after it.

Ian reports to Roark about the Aerodactyl. Officer Jenny reports to all the citizens of Oreburgh City that they are working on a plan to capture Aerodactyl, Kabutops, and Armaldo. Right now Officer Jenny and the researchers are facing Kabutops and Armaldo. Officer Jenny tells the researchers that a helicopter is searching for Aerodactyl, so they should focus on taking Kabutops and Armaldo down. The researchers agree. Suddenly, Ash and co. run up to them. Roark says that he will take care of Kabutops and Armaldo. Ash wants to help, too. Roark says that he will distract the Pokémon while Ash finds a way to take them down.

Roark sends out Cranidos, who uses Flamethrower to distract them. Then Pikachu and Sudowoodo charge towards the fossil Pokémon. Kabutops and Armaldo both use their attacks on Pikachu and Sudowoodo to get them out of the way. Cranidos then uses its Zen Headbutt attack. While it hurls its body towards Kabutops and Armaldo, three mechanical arms pop out and captures Cranidos, Kabutops, and Armaldo. Team Rocket comes out in a super-powered machine. The fossil restoration machine lies in the middle of it. Team Rocket says their motto. Ash wants to attack Team Rocket. Roark warns Ash that they have to be careful, otherwise Kabutops, Armaldo, and the fossil restoration machine could be damaged.

Suddenly, Aerodactyl swoops down on them. It uses its Hyper Beam attack to knock Team Rocket's machine off its feet. Aerodactyl's attack also frees Kabutops and Armaldo. This gives the researchers the chance to return the fossil Pokémon back into their Pokéballs. Aerodactyl then uses its Giga Impact attack. Cranidos tries to hold it back, but the attack is too powerful for it. Everyone is knocked to the ground. Aerodactyl uses Giga Impact again, and it is headed straight for Ash. Before the attack can hit Ash, a Bubblebeam counters it. Dawn runs up to them with her Piplup and Buneary. Brock notices that Aerodactyl is going to use Giga Impact again. Dawn has a plan to counter it. Just before Giga Impact can hit them, Piplup and Buneary jump into the air, and they spin around the attack to dodge it. Then they tackle Aerodactyl to the ground. One of the researchers throws a Pokéball and captures the Aerodactyl. Buneary picks the Pokéball and gives it to the researcher.

Team Rocket has managed to get their machine moving again. They notice that all the Pokémon are gone. Roark states that he wants the fossil restoration machine back. Team Rocket has no choice but to run with the fossil restoration machine. Cranidos chases after them. Meowth presses a button which fires a net to stop Cranidos. Ash and co. then chase after Team Rocket. Roark tells Cranidos that it can't let Team Rocket win. At this point, Cranidos begins to glow with a bright light. It evolves into Rampardos. Team Rocket is scared now. Rampardos grabs onto the fossil restoration machine and takes it away from Team Rocket. Then it finishes Team Rocket off with a Zen Headbutt attack. Team Rocket blasts off again.

Ash and Dawn notice that Rampardos is amazing and powerful. Dawn looks up Rampardos in her Pokédex. The researchers thank Rampardos for recovering the machine back. Officer Jenny even salutes Rampardos is a job well done. Ash asks Roark if he can have another rematch. Roark asks Ash if he has figured out a strategy. When Ash says yes, Roark accepts Ash's challenge. Ash then asks Dawn if she would help him train. Dawn agrees because the training will help her, too. With that in mind, Ash is more confident than ever to win his first Sinnoh badge.