On the way to Floaroma Town, Ash and the others hear some screaming nearby. At a house, a Pokémon hunter named J has just captured a girl named Melodi’s Gardevoir and she quickly flees the scene. Ash gives chase to her, and tries to battle her, only to have Pikachu frozen in stone and stolen just like Gardevoir. They decide to help Officer Jenny and try to help capture J, but eventually she also gets Meowth as well! Before she can take off, Ash, Jessie, and James sneak under her vehicle and follow her to her secret flying base. Now, the reluctant allies must work together to get back their Pokémon from J’s clutches.
As the heroes continue their path to Floaroma Town, they see a field of flowers. Suddenly, a Salamance passes by and Ash sees someone is riding it. The person comes off it and sends Ariados, who ties a woman to a tree and wants her Gardevoir. Gardevoir teleports, but the woman detects where it went and uses its equipment to turn it into a statue. A vehicle appears and it takes away the statue. The heroes untie the girl, while Ash goes to get the statue back. The vehicle is driven down on the road, so Ash and Pikcahu slide down a slope. Pikachu uses Thunderbolt, but the vehicle is too sturdy to have received any damage.
The person who stole Gardevoir is interested in Pikachu, as it displayed a lot of power. She sends Drapion and wants Pikachu to show some of its moves, as it will have a good price. Pikachu uses Volt Tackle, but misses. The woman is impressed and turns him as well into a statue. Ash is bound on a rock by Ariados' String Shot and witnesses that the woman goes away as his Piakchu goes away in the vehicle...
Team Rocket also sees this. They are nerved that woman stole Pikachu and plan to teach her a lesson. Brock and Dawn know that Pikachu got taken as well. Dawn sends Pachirisu, who uses Discharge to cut the strings Ash is bound onto. The vehicle stops and the man riding it comes out, as the smoke prevents him from going further. Team Rocket introduces themselves and get attacked by Salamance. The woman is interested in Meowth, who can talk. Seviper charges and James goes to send Carnivine, but Araidos' String Shot bounds him, Seviper and Jessie on a boulder. Meowth is also turned into a statue and got inserted into the vehicle.
The heroes pass Team Rocket (who are still bound on the boulder) and see a huge vehicle, which takes off and disappears, as if it was invisible. Jenny appears, as she heard she was here nearby. Jenny shows them she is a criminal by the name Hunter J. J has, like other Pokémon Hunters, stealing other people's Pokémon and selling them for money. Ash is very angered by this fact and promises to stop her. Jessie and James also want to stop her.
Inside the air ship, the driver of the vehicle allows Meowth to talk and records it. Meowth is given more time to think what product can he offer and the driver leaves him. Meowth wants to get his paws on the switch, as it controls him, Piakchu and Gardevoir. Ash asks Jenny where J went, but has no idea. Brock thinks they should be somewhere where J will surely be next. The woman (whose Gardevoir was stolen) sends Kirlia. Kirlia uses its powers to predict the place where J will be and Dawn sees a water wheel. Jenny reports to her superiors where J will strike next.
When they arrive, they see J is already taking an Absol. Ash runs to intimidate her and Jenny comes as well. Salamance uses Hyper Beam and Jenny's Arcanine uses Flamethrower, but Hyper Beam is stronger and hits Ash and Jenny. J leaves and the vehicle rides away, but not before Ash snuck under it. Ash sees Jessie and James came under the vehicle to get Meowth back. The vehicle goes to the air ship, which flies away.
Inside the air ship, Ash proposes to split up to search for the stolen Pokémon. Ash sends Aipom and they all split. The driver demands what product Meowth has thought about - Meowth offers to translate the Pokémon language. J is not interested, but sees the door is open - Aipom was overhearing everything. Aipom goes to Ash and they all go to the room where the Pokémon are. James presses a button and the door opens, revealing a room full of hunters. James runs away and finds Jessie, who is also chased by hunters and they turn to a hallway.
Ash and Aipom almost came, but Drapion grabs Ash. J is impressed, but cannot allow Ash to go away from the air ship. Aipom hits Drapion and frees Ash, who sends Turtwig. Drapion uses Poison Sting, but misses, as Aipom uses Swift and Turtwig Razor Leaf on Drapion. Drapion seems unhurt and retaliates with Cross Poison. Aipom sees a vent opening and everyone goes inside, including Jessie and James. The hunters enter as well, but Turtwig uses Razor Leaf to slow them down.
They all come to the room where the captured Pokémon are. They free Pikachu, Gardevoir and Meowth. The hunters also enter the room and the driver sends Golbat, who uses Steel Wing. Pikachu stops it with Volt Tackle. Golbat uses Supersonic, so Pikachu stops it with Thunderbolt, while also damaging a part of the wall. A force pulls everyone towards it, so they grab what they can. Ash calls Aipom and Turtwig back and sends Staravia, who goes to Officer Jenny to mark the location where they are. J hears trouble and orders to let the part of the ship go, even if some of her fellow hunters are in it.
The hunters go to get the Pokémon back, though the part of the ship falls. Just before the fall, Gardevoir teleported everyone away to safety. Ash sees they have been saved and Jenny captures the hunters. Team Rocket is impressed by J's abilities, but do not like her and will try to stop her if she gets in their way. J orders a new location for Pokémon to be captured. Dawn is still confused why would J steal Pokémon. Ash and Brock do not know the answer, but know Jenny will get her... someday.