Max leads the group through Petalburg Woods with his trusty PokéNav. However, his older sister May lags behind. She demands a break, and Ash concedes to another pit stop. Max alerts everyone that there is a Pokémon Center nearby. Brock is keen to meet the resident Nurse Joy so he grabs May's hand to pull her along. Yet May pulls away from Brock's grasp and falls backwards 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 isn’t quite convinced as he discovers part of a net embedded into one of the trees.
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 any Pokémon had recently been admitted to the Pokémon Center due to the activities of a Pokémon poacher named Rico, who frequents the area. 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 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 calls for them to be more creative. During Meowth’s talk he 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 the cage is 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 pre-evolved forms. Jessie is keen to create an Ekans army. Meowth points out that they cannot afford to feed them all, and Jessie replies that he and James will simply have to cut back, much to her teammates' horror. After being reassured that the Ekans will not be harmed, Arbok aims an Acid attack 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 arrives in a SUV. Introducing himself as Rico, he explains that the Ekans are his. He demands to know who they are, so the Rocket trio introduce themselves with their motto. 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 offers Team Rocket a deal, he'll leave them unharmed if they hand Arbok and Weezing over to him. Having gone through so much with Arbok and Weezing, and motivated by the imprisoned Ekans and Koffing, Jessie and James adamantly refuse. 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 them 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.
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 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 lowered to the ground, senses that Rico is near. Saying their goodbyes to Cacnea, the trio runs off.
Taillow soon locates 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 batters it with a Headbutt into the cage, knocking it out. Meowth manages to open the cage, freeing the Ekans and Koffing. Arbok and Weezing proceed to knock the poaching gun out of Rico's hands.
Angered, Rico sends out Pupitar, who promptly evolves into a Tyranitar. James orders another Smokescreen, and Meowth directs the Ekans and Koffing to flee into the wilderness. However Tyranitar fires off a Hyper Beam, and the warning shot stops everyone in their tracks. Jessie gets an idea and calls on Wobbuffet to Counter Tyranitar's attacks. Yet Tyranitar quickly knocks out Wobbuffet with a Hyper Beam before he can use the move. 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 Tyranitar's 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. Team Rocket latch onto Rico’s boots as he walks off, but he shakes them off and leaves them lying on the ground.
Afterwards, Rico is confronted by 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; however, he informs her that the poached Pokémon had escaped "thanks to a bunch of fools". Ash remarks how, with bad guys like Team Rocket around, there are still good guys in the world, unaware that the three Team Rocket members were the heroes this time.
By evening, Jessie and James walk through the forest, wondering if Arbok and Weezing managed to evade Rico. Although Meowth claims that all of the battling against Ash's Pokémon had hardened them against any threat, the pair remain feeling uncertain. Just then, the wild Cacnea who helped them out earlier reappears, carrying the same unopened bag of cookies. James kindly opens the bag up and hands Cacnea one of the treats. As Cacnea eats, Meowth comments that it is kind of cute, and Jessie agrees. When James asks if it would like to come with them, Cacnea happily accepts, accidentally poking James with its spines as it hugs him, which causes him to scream in pain.