When Team Rocket sits down for a delicious lunch at a noodle shop, the shop's owner asks to speak to them. The owner, Christopher, was a Team Rocket trainee along with Jessie and James—but after they took him to a noodle stand one night, he realized there was more to life than Team Rocket. Thanks to their help, he now has a noodle shop empire! And after he sees how Meowth's claws are perfect for slicing noodles, he even offers Meowth a job. But Team Rocket sticks with what they know best; they build a giant ramen robot to ambush Ash and steal Pikachu, only to get blasted by Pikachu's Thunderbolt.
Jessie and James blame Meowth for their defeat, so Meowth decides to go where it's appreciated: back to the noodle shop! Then, Jessie decides to be a full-time Coordinator, and she quits too! That just leaves James, heartbroken and alone, who hears our heroes talking about a uniquely colored Metagross in the mountains up ahead. James decides to catch Metagross for the boss, but he has no idea that this Metagross is known to be a deadly threat! Jessie hears about some poor Trainer who had an "R" on his shirt and went in search of the Metagross. It must be James, and it sounds like he's in danger!
Jessie runs to the noodle shop to get Meowth, but Meowth is a successful noodle master now. Meowth is still angry with Jessie, so Jessie decides to make it a solo mission. Up in the mountains, James has found the silver Metagross, but it easily defeats his Mime Jr. and Carnivine. Jessie's Yanma and Seviper get there just in time to knock Metagross away, but Jessie doesn't have time to celebrate her rescue. Metagross is tougher than they thought, and now it has both Jessie and James trapped—until Meowth arrives on the scene with a rocket and a getaway balloon. Metagross does use Gyro Ball to blast Team Rocket and their balloon into the sky, but Team Rocket is just happy to be a team again!
On their way to the next town and Snowpoint City, Ash and his friends are confronted by Team Rocket and their latest mecha with the goal of nabbing Pikachu. However, Ash casually has Pikachu use Thunderbolt to blast them away. Team Rocket land in the ocean and come ashore covered in seaweed. Though Meowth and Jessie are devastated by the latest defeat, James refuses to give up, suggesting that they beat Ash and the others to town. There, they are greeted by an aroma and come across a ramen shop. Despite being broke, they eat and attempt to escape without paying. However, this is aborted when they see Ash and the others, having shown up to grab a bite. They hide from them, but are found by one of the noodle makers, who tells the three the owner is demanding to have a word with them.
As the three are taken to see the owner, they beg for forgiveness and try to offer manual labor as compensation. However, much to their surprise, he refers to them as his mentors. It is then revealed that the shop owner, Christopher, was their friend and underclassman from their days at the Team Rocket Academy. Christopher reveals in a flashback that, after a tough day at the Academy, they went to a Ramen Noodle shop. There, Jessie and James told him there was more to life than Team Rocket, then treated him to a bowl of noodles. He became impressed by their kindness and how delicious the ramen was. After returning to Sinnoh, he opened up his own ramen shop, naming it "Jessie and James's Noodle Shop" after the ones who inspired him. Serving a thousand bowls of noodles in a single day, he soon had eleven of the most popular ramen shops across the entire Sinnoh region. He then thanks Jessie and James by offering them all they can eat for free.
When the noodle maker loses his grasp on a ball of noodle dough, it goes hurtling towards Meowth, who uses Fury Swipes on it. In doing so, he unintentionally slices the dough into perfect noodles, and Christopher is impressed. He asks Meowth to work for him, telling him that he is easily one of the best noodle makers ever and would eventually end up taking over the reins of the business. Meowth starts to picture the money and respect this would bring, but Jessie and James object, telling Christopher that Meowth is needed to build their mechas. Though he hated that Meowth's talent would go to waste, Christopher does not want to do anything to inconvenience his mentors and drops the matter.
Ash, Dawn, and Brock leave the town with the stomachs full and resume the journey to Snowpoint City when Team Rocket confronts them again, this time with a noodle-inspired mecha. They are zapped by Pikachu yet again, are blasted off, and repeat their previous landing. Jessie and James blame their failure on Meowth, which angers him. Meowth announces that he is going back to Christopher and train to become a noodle master. James tries to apologize, but Meowth still quits. James tries to chase after Meowth, but Jessie stops him, explaining that Meowth should be allowed to decide what is best for himself. Still upset, James contemplates losing Meowth while Jessie looks at the Ribbons she earned in the Solaceon and Majolica Contests. She decides to be a full-time Pokémon Coordinator, tells James that she is also quitting, and advises him that he should also consider leaving Team Rocket too, reminding him about his old background before leaving. A devastated James is left alone, and he yells into the sunset, vowing to climb to the top of the Team Rocket ladder by himself.
Later that night, James cries next to a fire, unable to imagine his life without his long-time teammates. He looks up and sees Meowth and Jessie in the stars, wondering what the two are up to. James then hears Ash and the others, and puts out his campfire so he wouldn't be seen. Spying on them, he overhears Dawn talking about an oddly colored Metagross living on a nearby mountain. Realizing that this would be ideal to give to Giovanni, James decides to catch it. However, he takes off so soon that he doesn't hear that this certain Metagross is very aggressive, and people who have previously tried to catch it have become seriously injured.
The next day, James climbs Metagross Mountain, where the Metagross lives. Two hikers take notice of him but do not try to warn him of the danger and proceed on their way. Later, as Jessie practices in the park with Yanmega, she overhears one of the hikers talking and learns about the aggressive Metagross and James' intent on capturing it. Realizing who they are talking about, she presses the two for more info, then hurries off to go tell Meowth. When she arrives at the ramen shop, it is packed with customers, and Christopher, not recognizing Jessie under her Jessilina disguise, tries to force her out. Noticing Jessie's presence, Meowth believes that she wants to talk him out of becoming a noodle making master, and thus doesn't want to listen. Devastated by his rejection, she tells him that she only came to congratulate him, and that he earned it before running out crying.
Back on the mountain, James calls out to Metagross, then sends out Mime Jr. as Metagross uses Psychic on some boulders. James commands Mime Jr. to use Teeter Dance and confuse Metagross. However, this backfires badly as the boulders Metagross used Psychic on fly out of control. James scoops up Mime Jr. and runs away, stopping just short of a cliff. Metagross corners James and Mime Jr., forcing James to call out Carnivine. After dealing with Carnivine's usual antics, he commands Carnivine to use Vine Whip. Metagross counters with Psychic, and James, Mime Jr., and Carnivine are ensnared in Carnivine's vines. Metagross then begins using Psychic to levitate them into the air and prepares to drop them over the cliff when Yanmega comes to the rescue with Steel Wing, which releases James and his Pokémon. Seviper then follows up with Poison Tail, and Metagross is knocked off the cliff.
Jessie laughs diabolically in victory, and James rushes over to meet her. As Metagross gets up, Jessie insults it, angering it and making it launch boulders at her and James. Jessie quickly uses Wobbuffet and its Counter to reflect the boulders back at Metagross. Metagross falls to its knees, but rises again when Jessie mocks it a second time. Metagross uses another Psychic and boulders hit them. Jessie and James recall their Pokémon retreat as Metagross gives chase. Metagross eventually captures them with its Psychic. Meanwhile, Meowth is interrupted from his thoughts and preparing noodles by the same two hikers. After hearing that his friends could be in danger, he presses them for information.
As Metagross prepares to finish Jessie and James off with Hyper Beam, they begin to accept their fate. However, they are saved by Meowth, who shot Metagross with a bazooka from the balloon. Jessie and James hop into the basket as Meowth begs for forgiveness. Just then, Metagross gets ready to use its Gyro Ball. Team Rocket tries to escape in their balloon, but Metagross strikes their balloon. Although they blast off again, the three are now in a happy mood, commenting that this did bring them back together. Then, they reaffirm their vow to one day successfully capture Pikachu.
Dawn sees them disappear in the distance, but mistakes them for a shooting star and then makes a wish to win her fifth Contest Ribbon. Ash comments that it was probably Team Rocket unsuccessfully attempting to capture the Metagross, and Brock replies that maybe it was or maybe it wasn't. Dawn tries to persuade Ash into making a wish to win his Gym battle, but Ash explains that there is no need to do so and that he and Pikachu will be alright.