On the way to Goldenrod City, Ash and his friends stop in a Pokémon Center to send his Tauros back to Professor Oak after using it in the Tauros competition. Oak tells him that Heracross is proving to be a very interesting research subject. After talking with Oak, Misty and Brock come up with Nurse Joy, who has finished inspecting Ash's Pokémon. Joy reports that they are all in excellent condition. Brock asks Joy to inspect him, but a nervous Joy conveniently remembers her duty to examine the Pokémon for something called the Fire and Rescue Grand Prix.
Curious, the gang decides to check things out. Apparently the Grand Prix is a firefighting contest for Pokémon and their Trainers. Always eager to show off his skills, Ash decides promptly to enter the contest with his own team. Misty reminds him that the only Water-type he has is Squirtle, but Ash is way ahead of her: he'll just use her Psyduck and Staryu. After an irate Misty complains that he should ask her first, Psyduck pops out. Ash interprets this as an expression of excitement.
Suddenly, a familiar voice calls to Ash and Misty. Captain Aidan and his Team of Wartortle greet them. Brock, who has never met Aidan or Team Wartortle, observes how well the Wartortle have been trained. Misty fills him in; while traveling in the Orange Archipelago, she, Ash, and Tracey met Aidan and Team Wartortle, the best firefighting force in the region. Ash's Squirtle had worked out with the team and even helped to put out a major fire. Aidan reveals that he and his team are the returning champions in the Fire and Rescue Grand Prix. The lead Wartortle shakes claws with Ash's Squirtle, its friend and rival.
The group goes to the work-out center, where Trainers and their teams exercise and practice before competing. Aidan has made it possible for Ash to enter the contest so late by telling the officials how good he was. Brock looks around at the other teams, noting that competition will be stiff. Ash, of course, isn't worried.
Then, Squirtle notices Officer Jenny and its old Squirtle Squad. Jenny notices that the Squirtle all look nervous. She assures them that they will do fine if they work as a team. Suddenly the Squirtle notice their former leader. While the reunited Squirtle Squad exchange happy greetings, Ash, Misty, and Brock greet Jenny. Jenny recounts how Ash and his friends converted the Squirtle Squad from ragtag delinquents to responsible and talented firefighters. At the mention that Team Wartortle are the returning champions, the Squirtle Squad expresses fear, at which Ash's Squirtle scratches its chin in an unimpressed manner.
Meanwhile, Team Rocket watches from a nearby window. They plan to steal all the Pokémon in the competition, including Ash's Pokémon.
While Ash's Squirtle continues to catch up with its old friends, Jenny asks if the Squirtle Squad can have a joint practice session with Team Wartortle. Aidan agrees, and both teams prepare for the target range, where Pokémon use their attacks to bring down targets. The Squirtle Squad looks very nervous as the practice begins. Aidan tells his Wartortle to focus on each target, listen to the lead Wartortle, and work as a team. The strategy works; each Wartortle aims with precision, taking down one target at a time with the concentrated Water Guns. In contrast, the Squirtle Squad seem out of focus. Their aim is off and they're not working with each other. While Jenny and Ash urge the Squirtle on, Brock observes that they're probably nervous being next to such a high-rated team as Team Wartortle. Ash's Squirtle decides to take action: it steps on each of the Squirtle's tails. Jumping up together in pain, the Squirtle finally aim as one like the Wartortle. Ash's Squirtle orders them to take down each target. When the practice ends, both teams have hit all the targets. The Squirtle Squad seem much more confident with their leader back. Ash notes that the Squad does not function without his Squirtle.
The Grand Prix finally starts, with Ash and his team - Pikachu, Squirtle, and Misty's Staryu and Psyduck - facing off against a team of Muk. The two teams will be competing to see who can put out a burning house faster. Misty encourages the team to show the Muk how awesome Water Pokémon are. Squirtle and Staryu aim Water Gun at the burning house, while Pikachu uses its back feet to fling dirt at the fire. Ash's team is working well, until Psyduck gets in the way of Staryu's Water Gun. The Pokémon is sent flying into the fire. Luckily, Squirtle rescues Psyduck before it becomes roasted. To apologize for its mistake, Staryu washes the smoke stains off Psyduck, who appears to have been unaware of its near-death experience. But the lost time proves to be fatal; the Muk team has extinguished the fire by covering it with their massive bodies.
After Ash's disappointing failure, the Squirtle Squad faces off against a team of Golduck, who apparently came in second place in the previous Grand Prix. Aidan worries that the pressure of the competition may be braking the Squirtle's concentration. His diagnosis proves correct; the Squad looks even more nervous than it did during the practice session. As the round starts, the Golduck team spring quickly and efficiently into action, with each Golduck taking one side of the burning house. The Squirtle Squad, on the other hand, appears too nervous to move. When they finally get going, one of the Squirtle trips and bowls over the others, bring them all down in a struggling heap. After managing to get to their feet, the Squad aim their Water Guns at their burning house, but the attack is weak and uncoordinated. At this rate, the Golduck will win easily. Concerned, Ash's Squirtle hurries up to Jenny, followed by Ash and Pikachu. Jenny's attempts to get the Squad to listen to her are futile, but then Ash comes up with a bright idea: Pikachu uses ThunderShock on the Squirtle to get their attention. Ash tells them that they need to listen to their leader. At this, Ash's Squirtle looks surprised, but Ash reassures it by saying that the Squad needs it. Squirtle takes control once again, and under its leadership, the Squad gets back into the fight. In the end, it's a close match, but the Squirtle Squad come out on top.
Suddenly, the extinguished fire reignites, and the house soon explodes. From the ground beneath where the house stood emerges Team Rocket in one of its giant contraptions. After reciting the motto, Team Rocket proceeds with their nefarious plan. Their machine, called the Torcher Scorcher, shoots flames out of its arms straight at the Squirtle, Jenny, Ash, and Pikachu. Aidan and Team Wartortle come to the rescue with the team's Water Guns, but James simply turns up the heat. Other Trainers start running towards the Torcher Scorcher with their Pokémon to try to help, but that was what Team Rocket was waiting for. Meowth presses a button and sends nets flying out from the Torcher Scorcher's body, ensnaring all the Pokémon - except the Squirtle Squad. Ash tries to run at the giant mecha, but Jenny pulls him away just in time to avoid the flames. As Team Rocket douses the stadium in fire, Ash tells his Squirtle that it must lead the Squirtle Squad to defeat Team Rocket and rescue the Pokémon. After a short huddle, the Squirtle Squad don the infamous glasses of its delinquent days and aim their Water Guns at the Torcher Scorcher. Team Rocket tries to step on the Squirtle, but Ash's Squirtle's orders keep its team members from getting crushed. Brock and Misty happily note the teamwork and superb timing of the Squad. Finally, Team Rocket gets dizzy from their efforts, and the mecha loses its balance and falls over. Squirtle crashes into Team Rocket's command station and blasts them against the wall with Water Gun. Then it stomps on all the controls, sending sparks flying. The door to the mecha's holding area opens, freeing the Pokémon. Squirtle jumps out of the Torcher Scorcher, but Team Rocket isn't through yet. The mecha gets up and prepares to blast Ash, Jenny, and the Pokémon with fire, but before Team Rocket can act, Pikachu and Squirtle combine their Thunderbolt and Water Gun attacks to blast the mecha. Team Rocket bids a bitterly painful farewell.
While construction trucks are busy repairing the stadium, Ash has a talk with his Squirtle. He says that the Squirtle Squad is very strong, but they need their leader. Ash's Squirtle looks sadly between its Trainer and its friends; Ash smiles encouragingly, and the Squad looks hopeful. Squirtle makes its decision: it will lead the Squirtle Squad like it did in the old days.
The Squad moves through the competition smoothly with newfound confidence. Team Wartortle also do very well. Finally, the final face-off begins, with the Squirtle Squad facing off against Team Wartortle. The challenge is to retrieve a dummy from a burning building and extinguish the fire in the least amount of time. Ash shouts encouragement to the Squad; Misty shouts good luck to the Wartortle; Brock shouts his support for... Officer Jenny. While Ash's Squirtle and the leader of Team Wartortle head into their separate buildings, their team members do their best to put out the fires. Then the leaders of both teams emerge with their dummies and direct their teams to put out the fire. The air is thick with tension as both teams race neck-and-neck. At last, the final Water Gun barrage extinguishes the fire in both houses, but who came first? Team Wartortle's total time is recorded to be 3:54:02, and the Squirtle Squad's time... is 3:53:00. As the stadium erupts with cheers, Officer Jenny and the Squirtle Squad celebrate their unexpected victory. Aidan and Team Wartortle congratulate the Squad with a salute, which they return happily.
At the end of the day, Ash congratulates his Squirtle. Jenny thanks Ash for letting his Squirtle leave his party and continue leading the Squirtle Squad. Squirtle says goodbye to Pikachu, Misty, and Brock, and then looks at Ash's other Pokémon. Chikorita and Cyndaquil both nod farewell, but as Squirtle holds out its claws to Bulbasaur to shake, Bulbasaur turns away. But then it extends a vine to its long-time friend, shaking solemnly. Jenny heads away on her motorcycle, with the Squirtle Squad riding in the back. As his Squirtle recedes into the distance, an emotional Ash yells that they will always be friends, no matter what. He remembers all the good times they had, from the moment Squirtle expressed its wish to join Ash's team to the present.
As Ash and his friends look on, they know that new friends and new memories await them...