As Ash and his friends are moving towards Rustboro City, May, wanting another break, slows down, causing everyone to stop for a break. However, when she leans back into a tree, she discovers that the tree bark has been torn in many places. Speculating as to what is going on, Max suggests that a Pokémon battle had taken place. Ash seems to agree, but later discovers part of a net embedded into one of the trees. Meanwhile, Max discovers that a Pokémon Center is nearby, and Brock proceeds to lead everyone else there.
When they arrive at the Pokémon Center, they meet Nurse Joy. May, believing that it is the same Nurse Joy from Oldale Town, tries to greet her, but is surprised when Nurse Joy doesn't recognize her. As Max tries to tell her that Pokémon Centers are run by a family of identical-looking Nurse Joys, Officer Jenny and her Growlithe appear to ask whether Pokémon had recently been admitted to the Pokémon Center due to the activities of a poacher named Rico, who is nearby. As Max also explains to May that Officer Jennys are also identical, Ash presents Officer Jenny with the part of the net that they had found. With a lead on Rico, Officer Jenny then asks Ash and his friends to lead her to where they found it.
Meanwhile, Team Rocket is on a hill overlooking the Pokémon Center. As they plan to trap Ash and his friends when they return, Meowth slips and rolls down a hill. At the bottom, he finds a cage full of Ekans. Learning that the Ekans had been caught and abused by a Pokémon poacher, Meowth tries to free them, but finds that their cages are electrified. At this point, Jessie and James, riding Arbok and Weezing, arrive. Outraged at how the Ekans are confined, Jessie orders Arbok to use Acid to free the Ekans, but Arbok is reluctant to attack its own pre-evolved forms. After being reassured that the Ekans will not be harmed, Arbok tries using Acid on the cage to melt it, but to no avail; Weezing tries to use Sludge to help. However, before Weezing can do that, it is attacked by a Fearow.
The Fearow's Trainer then arrives in a SUV. Introducing himself as Rico, he explains that the Ekans are his. Weezing suddenly discovers that Rico also has a cage full of Koffing attached to the back of his SUV. Rico soon explains that, under his client's request, he is to poach Poison-type Pokémon with a bonus for every evolved one he can get. He then says he will allow Team Rocket to leave unharmed if they leave Arbok and Weezing with him. Having gone through so much with Arbok and Weezing, and motivated by the imprisoned Ekans and the Koffing, Jessie and James refuse, and Arbok and Weezing prepare to defend themselves as Rico orders Fearow to attack. Fearow easily dodges Arbok's Poison Sting and Weezing's Sludge, and lands a Fury Attack on both. When Fearow tries to finish off Arbok with a Drill Peck, however, Arbok catches its beak with a Wrap. Just then, Rico withdraws Fearow for a Pupitar, who proceeds to use Sandstorm to send Team Rocket flying away. Claiming that Arbok and Weezing are too weak for his efforts, Rico leaves to poach more Pokémon.
Meanwhile, Ash and his friends arrive back at where they found the net. Max discovers tire tracks, and Brock surmises that Rico must not have gotten too far. Ash then sends out Taillow to search from the sky. Elsewhere, Team Rocket vows to free the Ekans and Koffing at any cost. Suddenly, a swarm of Kakuna and Beedrill appear, causing Team Rocket to run for cover. Ahead of them is a Cacnea, who brushes the Beedrill off with a Pin Missile. After thanking the Cacnea with a bag of treats, Jessie and James resign to the fact that Rico is now long gone. However, Arbok, with its body to the ground, senses that Rico is near. Saying their goodbyes to Cacnea, they run off.
Meanwhile, Taillow has located Rico in his SUV, and returns to Ash with the results. Unbeknownst to them, Rico is ambushed by Arbok and Weezing. Using Fearow to blow the smoke away, he discovers that Meowth had used the Smokescreen to sneak in and pick the locks off the cages, being able to withstand the electrified cage due to being subjected to Pikachu's attacks many times before. When Fearow tries to attack Meowth, Arbok uses Headbutt to send Fearow into the cage, knocking it out. Meowth then manages to open the cages and free the Ekans and Koffing, just as Arbok and Weezing use their attacks to knock the poaching gun out of Rico's hands.
Angered, Rico sends out Pupitar, who promptly evolves to a Tyranitar. Before Team Rocket can attack, Tyranitar attacks with Hyper Beam. Jessie gets an idea and sends out Wobbuffet to Counter Tyranitar's Hyper Beam. However, Tyranitar quickly knocks out Wobbuffet before it can set up an attack. With no other choice, Jessie and James order Arbok and Weezing to leave with the Ekans and Koffing, while they buy some time to allow them to escape. Though reluctant at first, Arbok and Weezing do so. Rico tries to use another Hyper Beam to cut them off, but Meowth attacks with a Fury Swipes to his face. Jessie and James also use their "Fury Swipes" to stall for time, although they get battered in the process. Arbok and Weezing watch in horror as they witness Team Rocket getting beaten up, and they tearfully leave with the Ekans and Koffing. Eventually, however, Tyranitar defeats the trio, and Rico leaves to look for the escaped Poison Pokémon.
Immediately afterwards, however, Rico is confronted Ash and his friends, as Officer Jenny tries to arrest him. Rico quickly sends out Fearow to resist the arrest, but Fearow is knocked out by Pikachu's Thunderbolt. Officer Jenny also orders Growlithe to knock the gun and Tyranitar's Poké Ball from Rico's hands. With Rico unable to evade arrest, Officer Jenny orders him to let go of the Pokémon he has poached, only for him to tell her that the Pokémon he had poached had escaped due to Team Rocket's actions. Ash remarks how, with bad guys like Team Rocket around, there are still good guys in the world.
Later, Jessie and James are seen walking through the forest, wondering if Arbok and Weezing managed to evade Rico. Although Meowth claims that years of battling Ash's Pokémon had hardened them against any threat, they are still uneasy. Just then, the wild Cacnea who helped them out earlier reappears, carrying the same unopened bag of cookies. When James asks if it would like to come with them, Cacnea obliges, poking James as it hugs him.