While they are still in Blackthorn City, Ash and friends are sitting on Clair's outdoor balcony at the Gym, eating breakfast with her. After some discussion, Ash plans to go to New Bark Town to register for the Johto Silver Conference now that he has all eight Badges even though the Silver Conference is in three months. Team Rocket has plans of their own, and they decide to steal Ash's Badges for their own purposes. Meowth and James want to sell the Badges, while Jessie wants to enter the Silver Conference using them. In the midst of their discussion Team Rocket's food is stolen, with Wobbuffet receiving the blame.
Jessie and James pose as a reporter and cameraman just as Ash and friends are walking out of the gates. Jessie takes Ash's jacket and hands it to Meowth, who is hidden behind a photographer's background, whilst James puts Ash into an oversized red coat and golden crown. Ash poses for several photos, and Meowth and Wobbuffet are admiring Ash's now stolen Badges. Jessie then returns Ash's jacket and begins to walk away. Ash utters the word prepared, and suddenly, Jessie and James stop in their tracks attempting to resist the urge to say their motto. Ash mentions the word trouble, and Team Rocket instinctively reveal their true identities. Meowth and James tell Ash that they have come for his Badges. Ash peers inside his coat, noticing that the eight Badges have been replaced with bottle caps.
Ash and friends give chase to Team Rocket, while Wobbuffet is further ahead with the Badge case and decides to rest on a marked ledge with a 'Jessie' flag on it. Wobbuffet then moves from its position, locating red Berry-filled trees. Wobbuffet imagines Jessie, James, and Meowth happily thanking it and stuffing their faces with the Berry. It fills the Badge carrying case with the Berries as a Wynaut watches hidden behind some shrubs. The Wynaut's appendages reach over and grab the case filled with the Berries and Ash's Badges. Wobbuffet quickly notices and the two Pokémon have an interchange. Jessie and the gang suddenly arrive, startling Wobbuffet and giving Wynaut time to flee. Unable to locate the case, Wobbuffet tries to explain what happened, with Meowth translating its accounts and Wobbuffet drawing a picture of Wynaut in the dirt. James believes that the drawing was of his childhood nanny, but after Wobbuffet states that the thief was blue, Jessie believes a Wooper stole the Badges, and they try to find one.
While Ash tries on his own to try to find the Badges. Clair mentions that Ash could have the Badges reissued. Ash acknowledges this, though states those particular Badges had special meaning and he begins to reminisce about all of his Gym challenges in the Johto region, from Falkner to Clair.
Team Rocket suddenly stumble across a Wooper sitting on a rock in the middle of a running stream. She attempts to grab it with her hands, but it dodges the trio and runs into the forest with Jessie, James and Meowth trailing behind. Meanwhile, Ash calls upon Noctowl and Bayleef to search through the forest, alongside Clair who is riding her Dragonair. Misty and Brock stay together whilst Ash goes in a different direction to find Team Rocket. Noctowl and Bayleef find Wynaut, the Badges, and some berries it has in a case. Wynaut is having trouble opening the case, so Bayleef lends its vines and returns the case back to Wynaut. With glee the blue Pokémon tips the contents of the case onto the ground, and to Bayleef's astonishment, Ash's Badges also fall out. Noctowl flies off, locating Ash by a stream and notifies him of the find.
Bayleef has since gathered the Badges on a large leaf. Wynaut's snack is suddenly interrupted when Wooper followed by Team Rocket appear. Team Rocket state Wooper led them there. Arbok and Victreebel are sent out to deal with the situation. Bayleef jumps backwards holding both Wooper and the leaf of Badges to avoid Arbok's Poison Sting. Victreebel's Vine Whip trips the fleeing Bayleef, separating it from the Badges. Jessie again calls for a Poison Sting attack, but the Wynaut's Counter intercepts, sending the attack back towards Arbok. Just as Meowth retrieves the Badges from the ground. Ash arrives on the scene. Arbok uses Poison Sting again, this time allowing Team Rocket to escape to their awaiting Meowth balloon. Bayleef's Vine Whip send Ash flying towards Team Rocket. He narrowly misses the balloon's basket, and begins falling to the ground. Noctowl quickly tries to catch him by the bag, but it slips from its grip. Clair and Dragonair then arrive to the scene and manage to rescue Ash.
Ash gets Noctowl to pick Pikachu up from the ground, reaching the escaping Team Rocket soon after. Pikachu lets out a Thunderbolt, and the balloon bursts sending Team Rocket flying. Ash and crew manage to rescue seven of the eight Badges, with only the Rising Badge missing. The group disperse once again to find the missing Badge in the surrounding greenery. Wynaut appears from the bushes, with the Rising Badge in hand, and hands it to Bayleef. Bayleef then gives the Badge to Ash who is searching nearby, when Bayleef tries to give credit to Wynaut for finding it, it disappears. A ship carrying logs suddenly travels past them through a stream nearby with Wynaut waving from it, though by the time Ash looks up, both the ship and Wynaut have passed through. Misty, Clair, and Brock gather near Ash, where he shows them that the Badge has been recovered.
The group later talks to Professor Oak via the video phone in the Pokémon Center. Ash announces that he has all eight of his Johto Badges. The call ends abruptly, however, when Ash's Snorlax, Kingler, Bulbasaur, and Muk become too enthusiastic, crushing Professor Oak. Now that Ash has all eight Badges, Clair tells Ash to follow a road to the sea, then to follow the coastline to reach New Bark Town, which she estimates will take a day or so, to register for the Johto League Silver Conference. The group wave goodbye to Clair and begin to head towards their next destination.
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