Now that Paul has won his badge from the Oreburgh Gym, it is Ash's turn to battle the gym leader, Roark. Ash asks Paul to stay for his battle. Paul doesn't want to stay because he knows that Ash will lose. Ash gets angry at Paul, but Dawn breaks it up before a fight can start. Dawn kindly asks Paul to watch Ash's battle. Paul doesn't recognize Dawn at all even though they met already, and this makes Dawn mad. Before Dawn can get into a fight with Paul, Brock holds her back. Ash asks Roark if he is ready to battle. Roark tells Ash that his Pokémon are exhausted from Paul's battle. He postpones the battle until the next day.
Meanwhile, Team Rocket is in the museum near the fossils. Meowth suggests that they study the fossils first before they steal them. Team Rocket gazes at one of the larger fossils in the museum. Suddenly, a man dressed in a lab coat walks up to them. He tells Team Rocket that the big fossil is his creation. His name is Kenzo, and he is one of the researchers in the museum. Because Team Rocket is also dressed in lab coats, Kenzo assumes that they are researchers, too. He asks Team Rocket which part of the museum they would like to see first. Team Rocket wants to see the fossil restorer creation.
Kenzo begins to lead Team Rocket into the research tower. Kenzo explains that in the research tower, researchers research the different Pokémon and how they evolve. Kenzo then states that after many years of research, his team has developed a machine that can bring fossil Pokémon back to life. Then Kenzo leads Team Rocket into the room where all the restored Pokémon are held. Team Rocket plans on stealing the machine.
Paul has finished healing his Pokémon at the Pokémon Center. He notices that Ash has all his Pokémon sent out. Ash is trying to decide who to choose for his battle with Roark. He finally decides to choose Turtwig because of its type advantage, Aipom because of its powerful Focus Punch attack, and Pikachu because of its Iron Tail attack. Staravia is sad that it didn't get chosen. Ash promises Staravia that it will be able to battle at the next gym. Brock noticed that Paul had his Pokémon use a lot of speed, which gave him an advantage. Paul walks up to Ash and co. and tells Ash that he should do the same as him. Ash clearly states that he never wants to be like Paul. Suddenly, a boy runs up to Paul and thanks him for the Azumarill. Ash can't believe that Paul gave his Azumarill away. Paul says that the Pokémon was a total loser, and it wasn't worth his time. This makes Ash even more angry. Ash hopes that he never loses to Paul again. He tells his Pokémon that they have a lot of training to do.
At night, Team Rocket is in their cabin making plans for their capture. Their plan is to capture the restoration machine that brings ancient Pokémon back to life. Team Rocket dreams of the riches they will soon have. They also plan on stealing a lot of fossils in the museum.
The next day has arrived. Ash and co. are at the gym, and Ash and Roark face each other. Paul is indeed watching Ash battle. Roark hopes Ash is ready for the battle. Ian explains the rules of the battle, and then it begins. Roark starts off by sending out Cranidos. Ash and Dawn are surprised that Roark would choose his best Pokémon first. Brock explains that Roark is testing out Ash's ability for surprises. It's a common technique for gym leaders. Ash doesn't seem to mind because all of Roark's Pokémon are rock types, but Cranidos has good speed. He sends out Aipom, and the battle begins.
Aipom starts off with Focus Punch. It jumps into the air and prepares for the attack. Cranidos uses Headbutt. It charges towards Aipom. When Aipom's Focus Punch is ready, it begins to use the attack. However, with Cranidos' great speed, it's able to hit Aipom first with its Headbutt attack. Ash and co. are amazed that Cranidos was able to jump far, too. Cranidos then uses Flamethrower. Aipom uses Double Team to dodge the attack. Then Aipom counters back with Swift. Cranidos dodges the attack. Then Aipom uses Focus Punch. Cranidos uses its Zen Headbutt attack. Both Pokémon collide into each other. Unfortunately for Ash, Cranidos has the upper hand, and it knocks out Aipom.
Brock states that Ash can now try to use his own strategy on Cranidos now that he knows what he's up against. Ash chooses Pikachu as his next Pokémon. Pikachu starts off with a Thunderbolt attack. Cranidos dodges the attack, and uses Zen Headbutt. It charges at Pikachu with blazing speed. Pikachu counterattacks with Iron Tail. It hits Cranidos, who falls into a pile of rocks. Cranidos quickly recovers from the attack. It charges towards Pikachu again with a Headbutt attack. Pikachu dodges the attack by jumping into the air, but Cranidos jumps into the air as well and hits Pikachu. Pikachu tries to use a Thunderbolt attack, but Cranidos hits Pikachu again but with a Zen Headbutt attack. Ash notices that Cranidos is so fast that Pikachu can't even prepare any moves. Ash wonders how he is going to be able to beat Cranidos since it's super fast.
Paul begins to see that the battle isn't worth watching since Ash is losing. He gets up and begins to leave. Before Paul can leave the battlefield, Pikachu supercharges itself with a bunch of electricity. Paul is surprised at the power Pikachu possesses, so he decides to stay. Ash tells Pikachu that it can do it. Pikachu uses Quick Attack. Cranidos then uses Flamethrower, but Pikachu dodges the attack. It speeds up towards Cranidos with fast speed and hits it with Iron Tail. When the smoke clears, Cranidos is still standing. Roark is impressed with Ash's strategy, however he isn't done yet. He orders Cranidos to use Head Smash. Brock explains that Head Smash is by far Cranidos' most powerful attack. Cranidos begins to charge up power for the attack. Ash isn't afraid. He orders Pikachu to use Volt Tackle. Both Pokémon charge at each other with all their might, and they collide into each other with extreme force. After the attack, both Pikachu and Cranidos remain standing. Ash knows that Pikachu is tired, so he calls Pikachu back.
Ash's final Pokémon is Turtwig. Roark knows that Turtwig has an advantage. Turtwig uses Razor Leaf attack, and Cranidos counters with Flamethrower. Turtwig dodges the attack and uses Bite. Roark and Paul notice that Turtwig is very fast. However, when Turtwig is close to Cranidos, Cranidos hits it with Zen Headbutt. Then it uses Flamethrower on Turtwig. Turtwig is able to withstand the attack. It jumps up and uses Razor Leaf. The attack hits Cranidos so hard that it faints.
Roark's next Pokémon is Onix. Ash sticks with Turtwig. Turtwig uses Razor Leaf. Onix dodges the attack and uses Double-Edge. Onix's body fully crushes Turtwig, and Turtwig faints. Ash returns Turtwig back into its Pokéball. Ash's only Pokémon left is Pikachu. Both trainers agree to give it their best.
Pikachu starts off with Iron Tail. Onix uses Slam, and both Pokémon collide into each other. Pikachu is worn out. It has taken a lot of damage from the battle. Ash knows that electric type moves won't work on Onix. Suddenly, Ash gets an idea. He orders Pikachu to use Thunderbolt on the whole field. Pikachu follows Ash's command. Onix then uses Double-Edge, however the rocks that are getting whipped into the air has slowed Onix down. Now is Pikachu's chance to attack. It charges towards Onix with its best Quick Attack move. Onix then uses its Screech attack to slow Pikachu down. The Screech attack is so powerful that it blasts Pikachu against a wall of rocks. Pikachu faints, and Roark wins the battle.
Roark congratulates Onix for a good job. Ash runs out to get Pikachu. Brock and Dawn are surprised that Ash lost the battle. Ash sees Paul walking out of the room and muttering, "How pathetic."