Ash may have lost his battle at the Oreburgh Gym, but he wants a rematch and he's down at the Oreburgh mine to train hard for round two. His hard work inspires Dawn to go back to town and train her own Pokémon for the upcoming Contest in Floaroma Town. But over at Oreburgh's museum, the fossil restorer machine has vanished, together with the fossil that was inside! It could only be the work of Team Rocket, who gets a big surprise when the stolen machine finishes reviving the fossil and a very irritated Aerodactyl emerges. After giving Team Rocket a good clobbering, it flies off toward Oreburgh City.
Aerodactyl causes a big commotion as it soars over the city, surprising Dawn and alerting the museum's scientists to the fate of their missing fossil. In the confusion, a Kabutops and Armaldo break out of their quarters and the scientists go to get Roark's help. Ash and Brock team with Roark to stop the rogue Pokémon, but Team Rocket appears and snatches Kabutops, Armaldo, and Roark's Cranidos!
Surprisingly, it's Aerodactyl who comes to the rescue—it swoops in and blasts Team Rocket once more, freeing the Pokémon and giving the scientists a chance to safely recall Kabutops and Armaldo to their Poké Balls. But now who's going to stop Aerodactyl? The guys all give it their best, but this time Dawn shows up to save the day! She has Piplup and Buneary team up to pin Aerodactyl so the scientists can put it in a Poké Ball. Then Roark's Cranidos evolves into Rampardos so it can take down Team Rocket, and the fossil restorer is returned to the scientists. All of which gives Ash an idea for his rematch with Roark...
Roark is pleased to see Ash has returned for a rematch, this time with added confidence. In the sidelines, Dawn unveils her special cheerleader outfit, and with the help of Piplup and Buneary, to cheer Ash onto victory.
Roark sends out his Onix. Ash opts for Pikachu and starts things off with Quick Attack. Onix replies with Slam, though Pikachu quickly dodges the attack and climbs onto Onix. Onix uses Screech to get Pikachu off, but it fails. Onix resorts to shaking Pikachu off, but he holds on tight. Pikachu quickly uses Iron Tail and hits Onix. Onix tries an Double-Edge, but Ash, taking a note from Dawn's technique, has Pikachu spin to evade and follows up with Iron Tail. However, Onix dodges the move, and smacks Pikachu into a Boulder with Slam. Onix uses Stealth Rock, setting things up for the future rounds. Pikachu uses Thunderbolt and destroys every rock near himself, also hitting Onix. Pikachu moves in to use Iron Tail and although Onix tries to stop Pikachu with Screech, Pikachu knocks Onix out with Iron Tail, winning the first round. Roark recalls Onix and sends out Geodude. Ash decides to recall his Pikachu and sends out Aipom.
Meanwhile, Team Rocket gets into the Oreburgh Gym thanks to Meowth's lock picking skills. However, their break-in attracts Brock's Croagunk's attention, who proceeds to look around. Soon, Aipom versus Geodude gets underway. Aipom aims a Swift at Geodude, but it counters using Rollout and proceeds to approach. Geodude misses its target and strikes a boulder instead after Aipom uses Double Team. Aipom leaps forward with Focus Punch, but Geodude blocks the attack with its strong hand. Geodude promptly uses Seismic Toss to smash Aipom into battlefield. Its follow up Rollout, however, fails after Aipom launches herself upright with her tail and performs a spinning dodge like Pikachu did. Aipom uses Focus Punch again, knocking Geodude out for the count.
Finally, Roark sends out his best and newly evolved Pokémon: Rampardos. Aipom uses Swift, but it doesn't affect Rampardos at all. Rampardos makes a swift reply with Headbutt, taking Aipom out. Ash sends out Pikachu again. Ash tells Pikachu to use Thunderbolt, but Rampardos dodges and uses Zen Headbutt. Pikachu tries to jump away, but is hurt by the Zen Headbutt as he spins past. Pikachu then sprints into a Quick Attack. Rampardos is about to use Headbutt, but Pikachu jumps over it. Rampardos throws Pikachu off with its tail. Pikachu returns with an Iron Tail, colliding with Rampados' Zen Headbutt. The physical contact temporarily paralyzes Rampados, but its Mold Breaker Ability nullifies the status condition. Rampardos uses Zen Headbutt one more time and Pikachu is knocked out. Elsewhere, Croagunk's intimidating stare scares Team Rocket out of the Gym. Jessie thinks that Croagunk wants to join their team, but Croagunk Poison Jabs her in the stomach. James and Meowth immediately pick her up and run away screaming to a hospital.
Now down to his last selection, Ash sends out Turtwig. Rampardos charges forward with Headbutt, but Turtwig rolls away. Rampardos is about to hit Turtwig with its tail, but Turtwig Bites down and tosses Rampardos away. Turtwig uses Razor Leaf, but Rampardos burns it with Flamethrower. Rampardos charges forward with Head Smash, rampaging through a Razor Leaf and battering Turtwig into a boulder. Turtwig uses Synthesis to heal itself while Rampardos is suffering recoil damage from its own Head Smash. Rampardos attacks again, this time with Flamethrower forcing Turtwig to stop Synthesis to dodge the attack. Ash begins to panic because all he can do is defend himself. Rampardos is way too fast and Flamethrower will negate any Razor Leaf thrown at it, but this suddenly gives Ash an idea. He orders Turtwig to start running while using Razor Leaf at the same time. Rampardos uses Flamethrower, but Turtwig keeps going and soon the burned leaves begin to obscure Turtwig. Roark soon realizes Ash is trying to camouflage Turtwig with the burned leaves, so he orders Rampardos to use Zen Headbutt again. Rampardos rushes forward, but Turtwig jumps away. Rampardos jumps, too, allowing Turtwig to roll underneath and stop behind its opponent. Rampardos is struck with Razor Leaf, knocking it out. Ian announces that Turtwig is the winner, earning Ash his first Sinnoh Badge.