While plotting their next scheme, the Team Rocket trio receives a video call from Team Rocket HQ. However, Matori answers instead, scolding the trio for not picking up quickly enough. Jessie is annoyed to see Matori instead of Giovanni and demands to know what she wants this time. As Matori says that the Boss is out on official business, Jessie simply hangs up on her. James is stunned by Jessie's actions, and calls headquarters again to receive the message. Matori gets straight to the point and reveals that Giovanni has ordered the trio on a special break, which leaves them all speechless.
Meanwhile, at the Cerise Laboratory, Professor Cerise prepares to send Ash and Goh to the Resort Area in the Sinnoh region. Ren reveals that the Resort Area has a large lake known to be hope to mysterious Pokémon known as the "Lord Pokémon". Sightings have attracted many Trainers to the area, and the prospect of catching the "Lord Pokémon" particularly excites Goh.
The Team Rocket trio arrive at their holiday destination, the Sinnoh Resort Area, hoping to relax and forget all about the twerps. However, they are stunned when Ash and Goh walk past. Goh even asks the trio for directions to the lake, not even recognizing Team Rocket in their casual clothes. Meowth spots another opportunity to catch Pikachu, though Jessie and James insist that they follow Giovanni's orders and enjoy their holiday. The trio try to distract themselves with some shopping in town, but encounter the twerps again. James asks what the pair are doing, to which Ash and Goh admit that they are looking for fishing rods. James leaps at the chance to help the boys purchase the correct fishing gear. Jessie, meanwhile, saves Pikachu from being hit by a passing skateboarder. Ash and Goh thank the trio for their help, though Team Rocket are left reeling from how close they got to finally catching Pikachu. They walk in the opposite direction after Meowth reminds his teammates that it is their mission to take a break.
Matori arrives at the Resort Area to meet with her waiting teammates, the Matori Matrix, to discuss Team Rocket’s next grand scheme. She reiterates that Giovanni wants to dominate the world, and so he will need powerful Pokémon to achieve his goal. Matori orders her agents to steal Pokémon from tourists across the Resort Area.
Team Rocket watch as several Trainers, including Ash and Goh fish at the lake. Goh soon feels a bite and reels in a Goldeen. He takes a moment to check his Pokédex before making an easy catch. Next, Ash gets something, which turns out to be a Magikarp. Goh is still hoping to see the Lord Pokémon, but catches Magikarp anyway. The boys begin to get disheartened as they continue to reel in more Goldeen and Magikarp, all of which Goh decides not to catch as he already has one of each. Goh hopes his Octillery lure might increase his chances of fishing up the Lord of the lake. Within an instant, Goh feels something heavy pull on his line. Ash decides help him reel it in, and the Rocket trio rush to assist as well. With their combined strength, the Lord Pokémon is pulled to the surface; a giant Magikarp. Goh is impressed by its sheer size and throws a Poké Ball to add it to his party. The attempts fails after Magikarp uses its tail to hit the Ball away. Goh decides he will have to weaken the giant first, so he calls out Oddish for a Grass-type advantage. As Magikarp starts Splashing on the spot, Goh calls for a Sleep Powder to send it off to sleep. Goh tries his luck again, and this time he catches the giant Magikarp. Goh thanks the Rocket trio for their help, to which they try to get away and continue enjoying their break.
Sudden explosions, however, in town get everyone's attention. As the Matori Matrix prepare to make off with their stolen load of Pokémon, Ash notices that Team Rocket are behind the theft. The Rocket trio spot Matori at the helm and are furious that they have been deliberately left out of the operation. Ash and Goh decide to intervene, so Matori leaves her Grunts to handle them while she returns to her helicopter. Goh's Raboot joins Pikachu and Riolu to assist against the menacing quartet of Rhyperior, Purugly, Toxicroak, and Skuntank. Pikachu and Riolu leap into action with Quick Attack and Vacuum Wave. Toxicroak sidesteps to avoid and poisons Pikachu with its Sludge Bomb. Riolu is knocked back by Purugly's Fury Swipes while Rhyperior hits Raboot with a Stone Edge. Pikachu fails to get up in time and is knocked down by a follow up Venoshock and Skuntank's Flamethrower. With the Flamethrower inferno keeping Ash at bay, one of the agents grabs Pikachu. A smokebomb goes off and the Matori Matrix manage to make a clean getaway with the Pokémon before Officer Jenny reaches the scene.
With Pikachu nabbed, Ash and Goh retreat to the local Pokémon Center to think things over. Meanwhile, the Rocket trio are determined to get their revenge on Matori and her elite unit for trying to steal the glory from them. To achieve this, the trio offer to assist Ash in getting Pikachu back. James reveals that he put a tracking device the grunt’s Skuntank during the earlier commotion. Ash agrees to the plan, unaware that Team Rocket are his newfound allies and plan to double-cross him and steal all the Pokémon for themselves. Thanks to the tracker, they soon reach Matori's camp and spot the cages of stolen Pokémon being patrolled by several agents. Jessie orders Goh to make the first move, allowing Ash and James to reach the cages while the guards are distracted. James uses his lock pick device to unlock the cage, freeing Pikachu and the other Pokémon. Ash gives Pikachu a Pecha Berry to cure his poison ailment. Goh, meanwhile, has his giant Magikarp use Splash to send the agents flying. The grunts crash back down, with the sound alerting Matori to the rescue effort. As Matori and the two remaining agents spot the emptying cage, James leaves the scene to remain undetected by Matori.
Matori underestimates Ash’s abilities and orders her agents to attack. Pikachu uses Iron Tail to counter Purugly's Slash attack, leaving it winded. Matori calls for the agents to make another move, but they soon find themselves surrounded and outnumbered by all of the freed Pokémon. The Pokémon combine their efforts and overwhelm the Matori Matrix, with Officer Jenny arriving to make the arrests. Matori is frustrated that this operation has been foiled and orders a tactical retreat. One grunt uses Rhyperior's Stone Edge to create a defensive barrier, allowing the Matori Matrix to escape Officer Jenny in their helicopter. The Trainers are soon reunited with their Pokémon, and Officer Jenny thanks the boys and Rocket trio for their help. With the presence of the Officer Jenny, Team Rocket decide to leave hastily. Goh asks about their name, leading Jessie to start reciting the Rocket motto. James and Meowth wave off the curiosity and intervene, dragging Jessie away.
Having returned to their Vermilion City base, the Rocket trio receive another call from headquarters. A particularly tired Matori appears on screen, and informs them that the trio's usual mission will now resume. Fully knowing about her failed mission, Jessie takes the opportunity to mock Matori for being tired and recommends she take a break of her own. Matori signs off while the Rocket trio are thrilled that they were able to stop Matori's scheme while remaining on top.
Back at Cerise Laboratory, the Professor and his assistants meet the giant Magikarp for the first time. Chrysa remarks that it appears the same as any other Magikarp despite its size. The giant Magikarp makes a massive leap, smashing through the Park’s glass dome and its landing leaves everyone soaked.
