Brock is back in Pewter City after his adventures in Johto, but he finds his father Flint hiding at the edge of town. Flint warns him that something terrible has happened: Brock's mother Lola took over the Pewter Gym and turned it into a gaudy Water-type Gym! When Brock sees this, he's furious, but Flint is afraid to act and Lola won't listen. So Brock declares that Flint will battle Lola for the Gym—if Lola loses, the Gym goes back to the way it was. But if she wins, all of Brock's siblings will become Water-type Trainers! With the Gym now a watery battlefield, Flint's Golem is at a disadvantage. Once Lola's Marill uses Surf, Golem sinks like a rock, and Lola's Blastoise has to fish it out of the water. When Flint starts to walk away, dejected, Lola reminisces about their first battle together. This rekindles their love, but Brock doesn't care. He's not even impressed when Flint and Lola try to patch things up by making the Pewter Gym a Rock-and-Water-type Gym.

Misty has returned to Cerulean City to step in as the Cerulean Gym Leader. But as soon as she arrives, she hears a news report about the Pokémon Investigation Agency closing Gyms that fail to meet proper standards—and rumor says Cerulean City is their next stop! Unaware that three of her enemies are in town, Misty rushes to the Gym and finds an out-of-control Gyarados in the pool. Neither Nurse Joy nor her sister's fan club can control it, and she can't just stick it in its Poké Ball while it's still upset. It's Misty's duty as Gym Leader to solve the problem, except she's also had a Gyarados phobia ever since she was a baby! Misty puts on a water show costume and swims in the pool, hoping to stir Gyarados's memories of performing together back when it was a Magikarp. Instead, Gyarados turns the pool into a raging whirlpool, and Misty blacks out. As her Horsea rescues her, she dreams of Ash and Brock telling her she can do this on her own.

From his castle high on a hill, a mad scientist dispatches a giant robot to the village below. The villagers sound the alarm, afraid that the robot will ruin their crops, and a girl named Kate hopes that the angels of justice will save her village. Instead, Team Rocket—fresh from being blasted off by Pikachu—land right in front of the villagers, and Kate mistakes them for the superheroes known as Team Righteous. To convince the villagers of their villainy, Team Rocket knocks the robot out of commission. That just convinces everyone that they really are heroes! The grateful villagers tell Team Rocket that the stranger in the castle keeps sending robots to destroy their fields during the harvest season, and they want Team "Righteous" to protect them. Surprisingly, Jessie thinks this is a great idea; they'll fool the village and turn it into Team Rocket territory. Meowth makes a Meowthmobile mecha out of the robot they destroyed, and Team Rocket heads for the castle.

At Professor Oak's lab, Tracey and the Professor are busy with their daily work. So busy that they don't even notice when a Team Rocket helicopter lands on the property—Butch and Cassidy are here, and they plan to steal all the stored Pokémon from the lab! While Ash's mom Delia stops by to say hello to Professor Oak, Butch and Cassidy put on Pokémon disguises and make their way toward the lab. The local Pokémon take an interest in these new visitors, thinking they're real Pokémon, but an Oddish realizes the newcomers are just people in costumes. Oddish alerts Bulbasaur, who decides to take action. It grabs Tracey and sends Noctowl to scout the area for signs of the intruders. By the time Tracey realizes what's going on, Butch and Cassidy have already looted the Poké Balls from the lab and left the building. Now they're back in their Pokémon disguises and headed for the helicopter, but they're slowed down by a lovestruck Nidoking and an affectionate Muk.

Misty has a problem: her Psyduck can't swim. It doesn't even like water! So when Tracey stops by the Cerulean Gym for a visit, the two Trainers give Psyduck some swimming lessons, with absolutely no success. Then Sakura, a familiar face from Ecruteak City, stops by the Gym to challenge her friend Misty and earn the Cascade Badge. That's when Misty gets a big surprise: the Gym ran out of badges, and her sisters forgot to tell her! The Cascade Badges are made by an artisan in Rifure Village, so Misty, Tracey, and Sakura head out to find him. Near the village, they rescue an injured man who turns out to be Kinzo, the very man they need. Even with an injured ankle, Kinzo is a tough old man. He won't just hand over the badges; he wants everyone to work for them. That means waking up at 4 AM to run laps, split wood, and craft their own badges. If they don't do it right, they'll have to wake up the next morning and do it all over again!

In the middle of a busy city, the Pichu Bros. are summoning their friends—Smoochum, Wooper, Magby, and Teddiursa—to play. Meowth is in town, too: it's taking a vacation from Team Rocket and dreaming of building a monument to itself. It sets out with a picnic basket to look for place to build its statue, but trips over Smoochum along the way. Smoochum has its own basket of accessories, and it accidentally walks away with Meowth's basket instead. When Meowth chases Smoochum to get its picnic basket back, Smoochum runs to the alley where all its friends are, and everyone plays keep away with the basket. Meowth finally grabs the basket, but then it steps on a sleeping Houndour and ends up running for its life. Its basket rolls into Teddiursa's path, and Teddiursa eats everything before Meowth can get the basket back.

Ash's friend Richie has come to Professor Oak's lab to ask for advice, but Tracey is the only one home; the Professor is on Seafoam Island for a live TV appearance. At least, that was the idea—when Tracey calls for an update, DJ Mary tells him that Professor Oak has vanished! Tracey and Richie head to the TV station to find out what happened. According to DJ Mary, Professor Oak made it to the morning rehearsal, but after two strangers pulled him away to ask a question, he was never seen again! Security didn't see the Professor or the strangers leave the station, but Richie realizes that the kidnappers posed as deliverymen to get in and out of the building. Indeed, it's just as Richie thought, and Butch and Cassidy are the ones behind the plan. Dr. Namba wants to force the Professor to tell him where to find Pokérus. Namba needs samples of the Pokérus virus to help him with the Pokémon Power Acceleration Project, but Oak refuses to give up the information.

Meowth wants to enjoy the last days of its vacation with a picnic lunch in the park. But Meowth's sandwich starts floating in the air, and it zooms away when Meowth tries to chase it! Meowth chases the sandwich through the park and runs right through the special reception Azumarill is preparing for Azurill, who is coming from out of down. After a commotion like that, all the Pokémon friends end up chasing the sandwich! When the sandwich goes flying, Teddiursa catches it and gobbles it down in one gulp. The other Pokémon spot a footprint that suggests it was an invisible Pokémon who first swiped the sandwich, but who? Just then, Meowth sees a strange red stripe floating by. This must be the invisible Pokémon! One of the Pichu Bros. asks a Smeargle for help, and Smeargle throws paint around until the invisible Pokémon is covered in paint and plain to see. It's a Kecleon! Kecleon runs away, but its paint-covered footsteps lead the others to a empty pipe.

Cerulean City is where all the action is: Misty's sister Daisy is back, Butch and Cassidy are coming to steal a Delcatty, and both Tracey and Casey, the baseball-loving Trainer from Johto, are visiting the Cerulean Gym. They're there when a Pelipper delivers a letter to Misty, asking her to meet someone named Georgio by the lighthouse. While Tracey is stuck with pool-cleaning duty, Casey and Misty go to meet the mysterious Georgio. He turns out to be a young Trainer who wants to ask Misty on a date! He even has two great tickets to tonight's Electabuzz vs. Starmies game, the one Casey wants to see. Misty says no, but Georgio offers to battle her—if he wins, Misty will go the ballgame, and if not, she'll never have to see him again. Misty agrees, but when Georgio sends out his Delcatty, Butch and Cassidy grab it! They were hiding at the top of the lighthouse, and now they make their escape on hang-gliders.

In the middle of being blasted off again, James finds a bottle cap from his training days that starts everyone reminiscing about being Team Rocket trainees. Jessie was a problem trainee, unable to work with any partner for long. Meowth walked into Giovanni's office, asking to be made a Team Rocket field agent. And Butch and Cassidy were trainees, too—Cassidy was Jessie's constant rival. Drill Sergeant Viper ordered Jessie to start training with her new partner, James, and Meowth was assigned to their team after Giovanni lost patience with its incompetence. In their first team challenge, they had 24 hours to reach a target location in the wilderness, surviving on a loaf of bread and bottle of water per person. When Meowth ate all its food right away, James shared his food with Meowth. Jessie sniffed at such sentiment, but when they made camp that night, she reluctantly shared her own food with the other two. The next day, the trio had to cross a rickety bridge.

Richie and Sparky are in the big city, where the nearest Pokémon Center is scheduled for demolition. Two Nurse Joys—a grandmother and granddaughter—are trying to stop the demolition crew, so Richie and his Pokémon step in to drive off the crew's Pokémon. The Nurse Joys tell him that this Pokémon Center opened 75 years ago, back when the area was a rural place where Celebi lived. That was the same day the elder Nurse Joy's friend, Nick, was lost in a landslide. That night, a Celebi appears before Richie and shows him a Celebi carving hidden in the Pokémon Center's furniture. Then Richie is surrounded by light, and the next thing he knows, he's in the middle of a forest! Richie hears a cry for help, and he rescues a young Joy from falling off a cliff. Joy leads him to the local Celebi shrine, where he's introduced to her friend Nick. Richie is in the past—and it's the day before the Pokémon Center first opened!

A peaceful day at Professor Oak's lab turns into chaos when a series of small incidents leads to a Tauros stampede! The mayor's son, Gilbert, is supposed to receive his first Pokémon, but the Tauros broke through the walls of the lab and now the starter Charmander, Squirtle, and Bulbasaur have all escaped. And when Gilbert does show up, he has a lot of attitude but very little affection for Pokémon: he just wants something cool and powerful, not a Kanto starter Pokémon! However, everyone's first priority is to catch the runaway Pokémon. Tracey and Ash's mom Delia will go one way, Professor Oak, Gilbert, and Ash's Bulbasaur head for the mountains. In the forest, Tracey and Delia rescue Charmander from a stream. Up in the mountains, Gilbert is scared of the high, narrow path, and is ready to walk away even after he spots Squirtle stuck on a tree overhead.

Professor Oak and Tracey are visiting the island where Gary is currently doing research. But not only are Butch and Cassidy tracking their movements, the Professor and Tracey encounter a raging Aerodactyl the minute they arrive on the island! The researchers on the island study ancient fossils, and Gary had the idea to use a piece of amber and a fossilized Egg to revive ancient Pokémon. However, as soon as they revived Aerodactyl from the Egg, it escaped and went on a rampage! Crystal, the little sister of head researcher Dara, asks all her Pokémon friends on the island to help look for Aerodactyl. Sure enough, one of the Farfetch'd sees Aerodactyl and leads everyone to the spot. Aerodactyl is sleeping near the spot where the fossilized Egg was found, but it wakes up and flies off. Tracey tries to grab onto it, only managing to jump off after a wild ride.

Team Rocket agents Butch and Cassidy have just received their latest orders: steal a Luvdisc from the Cerulean Gym! There are two Luvdisc at the Gym, including a new one that Daisy brought, and Tracey has stopped by the Gym to take a look. The Luvdisc are Luverin and Kasurin; Kasurin likes Luverin, but Luverin's not interested. This could jeopardize the romantic underwater show that Daisy has planned, but things only go truly awry when Butch and Cassidy break into the Gym, grab Luverin, and run for it. Kasurin is able to sense Luverin, so Daisy, Tracey, and Misty take Kasurin with them and set off after Team Rocket by car and inflatable raft. Kasurin tracks Luverin to the scattered islands where Team Rocket have a secret lair, but Butch and Cassidy know the good guys are coming. They steal Kasurin, them dump our heroes in a pit trap! What's worse, Misty and Tracey left all their other Pokémon at home, so Misty must encourage the two Luvdisc to break out on their own.

After the Electabuzz's 10th loss in a row, Casey is upset about the fortunes of her favorite baseball team. With star pitcher Corey Demario sidelined by a shoulder injury, there's no relief in sight for the Electabuzz! But when Casey sees a runaway Charizard in the park, she realizes its Trainer is none other than Corey Demario himself. During his recovery, he's helping out his father, a Pokémon rancher. The Charizard, Don, really belongs to a boy named Benny, but Corey raised it—and now he's trying to help Don, who's so insecure it can't even fly or use Flamethrower. Naturally, Casey offers to help Don regain its righting spirit. Back at the ranch, Corey's dad tells Casey that Corey's arm is fine, but Corey's lost the confidence to go back to pitching. Helping Don was supposed to help Corey too, but the plan hasn't worked, so now it's up to Casey. Casey starts by making everyone do some cheerleading, then orders Don to battle.

Richie is on the S.S. Anne when a school of wild Gyarados block the waters ahead. The crew is about to take the long way around, but a grizzled Trainer named Silver orders his Salamence to send the Gyarados packing so the trip can continue. Silver also has a Chikorita, and a lifelong mission: to battle the Legendary Moltres! But Richie thinks there's something suspicious about the two researchers with Silver, especially when the ship docks at an evacuated volcanic island and Richie sees the three of them sneaking onto the shore. Richie jumps ship and follows them, convinced something is up. When he catches them headed for the top of the volcano, they tell him Moltres should appear at this volcano tomorrow. The researchers want to sample Moltres's fire for scientific reasons, so they enlisted Silver's help—and they don't want Richie tagging along. However, Richie later overhears the researchers talking, and they're really Butch and Cassidy!