Team Rocket spots Ash and his friends walking by and put their latest plot, the PokéPod into action. They pose as inventors struggling to test their invention. Ash kindly offers to assist the pair of scientists, and Jessie promptly places Pikachu inside the PokéPod, and the device locks itself automatically. James declares the device to be a total success, and now cannot be opened without the key. Ash asks for Pikachu back, but Team Rocket reveals themselves to Ash and quickly makes a getaway using Weezing's Smokescreen as cover. The group gives chase, however, Jessie is able to pass the PokéPod to her hiding Wobbuffet unnoticed by Ash and the others. By the time the group catches up, they are surprised to see that the PokéPod is gone. Though Wobbuffet accidentally reveals himself and blows the clean getaway. Ash makes a run at the Pokémon, causing Wobbuffet to panic and accidentally trip on a nearby rock. While the PokéPod containing Pikachu goes flying into Ash's arms, Wobbuffet falls into the nearby river and is quickly swept over a waterfall, along with the key needed to release Pikachu.
Ash tries to force the lock open, and Jessie admits that Wobbuffet has the only key, and thus the only way to release Pikachu. Team Rocket gets upset that they may never see Wobbuffet again, and Meowth demands Pikachu as compensation. Ash, of course, refuses, but Jessie tries to manipulate him further. As she proposes a deal that whoever recovers the key first will get Pikachu, James cuts Jessie off by pointing out that the twerps have already left to find Wobbuffet. Team Rocket quickly takes off too, knowing that the first to find Wobbuffet and the key will also get Pikachu.
At the falls, Ash and the group struggle to find a way safely down while Team Rocket sails by in the Meowth Balloon. Wobbuffet enjoys the gentle current and takes the time to look up to the clouds where he sees Jessie's image among them. His gentle downstream venture ends when he bumps into a Quagsire and gets a fright. Quagsire points out the directions to a nearby forest, and Wobbuffet leaves the river to wait for Jessie to catch up. Team Rocket soon spots him walking off, just as Ash, Brock and Misty notice him too. The two groups soon lose sight of Wobbuffet, who starts swinging on some vines from tree to tree. Ash runs after him but falls down a steep hill and onto a road. Brock and Misty catch up, as Team Rocket also crashes down. Wobbuffet also apparently had a bumpy ride and is now hanging from a branch above the road. He is happy to see Jessie and begins to lose his grip as a massive truck speeds around the corner. Jessie tells Wobbuffet not to let go, but it's too late and Wobbuffet falls directly onto the speeding truck. As Wobbuffet hangs on, several police cars round the bend and Team Rocket soon disappears from the law. From the lead car, Officer Jenny explains that they need to catch the truck and Ash tells her they need to as well.
Soon the situation is explained and Jenny allows Ash and company to join her in the pursuit of Goneff, a master thief who breaks into bank vaults with the assistance of his Golem. Brock, as usual, tries to flirt, but Misty painfully reminds him that she's got enough problems already. A roadblock has been set up to catch Goneff as he nears a bridge, leaving him with no escape. As Goneff tries to shake off the police, the sudden turns cause Wobbuffet to fall onto the windshield. Goneff tries to get the blue blob off, but to no avail and the distraction causes him to run right into the roadblock. The truck crashes through several police cars into the city, and Officer Jenny has all the bridges raised and all avenues of escape cut off. Soon the truck is surrounded by the police as well as Team Rocket who approaches from the balloon. It appears the jig is up for Goneff, however, the thief has a trick up his sleeve, and the container on his truck opens up to reveal a covert Golem hot air balloon inside. Goneff jumps aboard to make his getaway but realizes that he has a stowaway, Wobbuffet, who he then tries to throw out. However Wobbuffet uses Counter to instead send Goneff flying right into the hands of the police as the Golem balloon starts to fly away with Wobbuffet still on board.
Giving chase in the Meowth balloon, Jessie tries to recall Wobbuffet into his Poké Ball. Though the Golem balloon is flying wildly and the recall beams don't make contact with the errant Pokémon despite James moving them as close as possible. The balloon suddenly suffers a puncture as it hits the corner of a building and Jessie has Meowth cover the hole. The Golem balloon then appears over Team Rocket’s own balloon, so Wobbuffet tries to leap to Jessie. Wobbuffet instead lands directly on the Meowth balloon, causing it to subsequently deflate, which sends the Rocket trio blasting off in one direction and Wobbuffet in another.
Ash is now trying to smash apart the PokéPod, but it appears that it is indeed impervious to damage and the key is indeed the only way to release Pikachu. Suddenly Ash sees Wobbuffet and the key flying overhead. As Wobbuffet is about to fall into the river, Ash sends out Chikorita and has her use Vine Whip to catch Wobbuffet. This works until Wobbuffet and the key become snagged onto the raised bridge, and he subsequently lands in a passing speedboat. Ash and the others give chase, and soon the Rocket trio joins the pursuit. Jessie orders Wobbuffet to hit the brakes, but he is knocked out cold from his earlier collision into one of the drawbridges. Ash and Jessie the leap into the speedboat, just managing to stabilize their balances. Wobbuffet then recovers, but it also snaps the steering wheel off in the process followed by the throttle stick. Meanwhile, Goneff has escaped again, this time on one of the officer’s own motorbikes. Ahead of the speedboat is a Lapras-shaped cruiser which causes it to go flying and Wobbuffet to be thrown onto the back of Goneff's bike. As Goneff curses his luck, the speedboat is about to crash into a bridge when Ash uses Totodile's Water Gun to slow it down.
Regrouping, Ash and Jessie learn that Wobbuffet is being held hostage by Goneff who is holed up inside an abandoned building demanding a helicopter in exchange for its release. As Officer Jenny and the police surround the abandoned building where Goneff is holed up, Team Rocket works out a plan to get them past the good guys. As Goneff, his Golem and a bound Wobbuffet wait for the police response, Ash and friends sneak around the back and find a tunnel dug inside the building. Team Rocket suddenly appears in front of Goneff where they recite their motto. The trio offers Goneff a deal, their escape tunnel in exchange for Wobbuffet. Goneff refuses and sets Golem onto them, intending to use the tunnel and leave Team Rocket high and dry in the hands of the police. Suddenly Ash appears with Totodile demanding Wobbuffet's release. Goneff sends Golem after Totodile, and despite the fact that Golem is at a disadvantage typing-wise its sheer strength overpowers Totodile. Goneff tells Golem to use another Tackle. Totodile prepares for impact and hides behind Wobbuffet, who uses Counter, freeing himself from the rope. The Counter attack also sends Golem flying into Goneff, who crashes out of the building and is quickly arrested by the waiting police.
As Ash congratulates Totodile on its quick thinking, Wobbuffet rejoins the rest of Team Rocket and they make a getaway with the key needed to free Pikachu. Ash and Totodile chase them, only to find them leaving in a Wobbuffet-shaped balloon. Ash demands the key, however Wobbuffet is now inside his Poké Ball and Team Rocket boasts that now it's their turn to be chased. However Wobbuffet suddenly emerges from his Poké Ball, as he often does, and Ash takes the chance, sending Noctowl to pop the balloon. Noctowl does so, and as Team Rocket is shaken about the key falls off Wobbuffet and is sent towards the ground. Jessie, James, and Meowth all separately try to grab it, but can't do it before Ash finally grasps it in his hands. Pikachu is quickly released from its PokéPod prison. Team Rocket sadly realizes they've lost as Ash has Pikachu send them blasting off with a Thunderbolt. Ash thanks Officer Jenny for her help, and she salutes the group for leading to Goneff’s arrest. Ash and his friends continue on their journey. Meanwhile, Jessie, James, and Meowth struggle to hang onto a bridge while Wobbuffet is standing safely on the top. As they beg for his help, Wobbuffet is just happy to relax after his adventurous day.