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!

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!

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.

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!

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.

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.

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!

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!

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.

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.

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.

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.

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!

Team Rocket agents Butch and Cassidy have just received their latest orders: steal a Luvdisc from the Cerulean Gym!

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!

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. 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.