Walking though a dense, fog-covered forest, Ash, Misty, and Brock are headed for New Bark Town where they hope to get registered for the Johto League. Lost, Misty blames Ash for walking in circles. Brock tries to break the two up, but it only creates more controversy. Amongst the arguing, Pikachu and Togepi wander off to see a Suicune stationed at a nearby lake. The gang closely follows as they all witness this rare sight, but after spotting Ash, the Suicune flees. Running after it, the group trips as they stumble down a steep hill.
Meanwhile, Jessie, James, and Meowth have just found their way out of the same forest. Desperate for food, they come across what seems like a Pokémon University. After giving it some thought, Jessie realizes that they must have some kind of cafeteria inside. Hearing somebody enter his lab, the preoccupied Professor Elm mistakes Jessie for Nurse Joy and tells her to check up on his Totodile. Naturally, Team Rocket steals it and runs off.
Ash finally reaches New Bark Town and runs off to face the Johto League. Brock reminds him that he has to register at the Pokémon Center first. Anxious to see Nurse Joy, Brock is confronted her Chansey instead. Disappointed, Brock's attention is drawn to a monitor stating that Joy is with Professor Elm, and she'll return at 2:00. Misty notes that it's already 3:30, so Brock gets a little concerned. Believing that something must be wrong, he forces group to set off and find her. Reaching Elm Laboratory, which is now swarming with police, Brock flirts with the local Officer Jenny. As usual, Misty drags him away. Inside, Ash and the others see Nurse Joy scolding at Elm for being careless.
Jenny tells Ash that the Totodile is supposed to belong to a trainer that's starting her Pokémon journey tomorrow. Elm explains that in New Bark Town you can choose from a Chikorita, Cyndaquil, or Totodile. Ash says that from where he hails from trainers can start with a Bulbasaur, Charmander, or Squirtle. Elm realizes that Ash must be from Pallet Town, and he most likely knows Professor Oak. Ash complies, and asks Elm if he's ever met him. Shocked, Elm explains that he was one of Oak's best students, and in a way, he's his biggest rival. Instead on focusing on the study of human and Pokémon relationships, Elm concentrates on Pokémon evolution. Ash tells Joy that he has to register for the Johto League, and she apologizes for not being back at the PokéCenter on time. Ash tells her that it's okay because he knows how exciting it is to get your first Pokémon, and that's why he'll help Jenny find the culprits. One of the officers comes up to Jenny and reports that they made a plaster case of some footprints outside of the lab. At the same time, Team Rocket runs down the street panicking as Totodile has attached itself to Jessie's hair with it's mouth.
Using the scent from the plaster case, Jenny's Growlithe picks detects Team Rocket and closes in on their position. Meanwhile, Jessie tries to detach the Totodile from of her hair, but she has no luck. Meowth decides that he'll make the call to tell the boss about their new discovery, but Jessie stops him because she knows that Meowth's nature is to take all the credit. As Jessie and Meowth argue, James casually walks past them and starts to make the call. James forgets the boss's area code, so he asks Jessie and Meowth for it. They start beating on James as well.
Growlithe finds Team Rocket, and Jenny declares that they're all under arrest. Team Rocket tries to flee, but Ash summons Bulbasaur to stop them. It uses Vine Whip, tripping Team Rocket. James sends out Weezing to use a Smokescreen attack, but it's stopped short when Ash's Charizard uses its wings to blow the smog away. Bulbasaur then uses Vine Whip to pull Totodile off of Jessie's hair. Jenny then tells Growlithe to attack, but Weezing uses Sludge and Growlithe is disabled. Seeing that they have the advantage, James quickly dispatches Victreebel. As usual, it attacks James instead of its target. Lickitung is next to come out, but Ash commands Squirtle to use Water Gun. It connects. Jessie then accompanies Lickitung, Weezing, and Victreebel with Arbok as they attack simultaneously. Fighting fire with fire, Bulbasaur, Charizard, Pikachu, and Squirtle combine their attacks, which creates a gigantic explosion, blasting Team Rocket's Pokémon over the horizon. As the smoke clears, Jessie and James are terrified. Totodile steps in and releases a Water Gun, sending Team Rocket through the stars.
Back in the PokéCenter, Ash gives Oak a phone call reporting his discoveries. Elm takes over the conversation and has a very long chat. Totodile walks away from Elm, and goes up to Nurse Joy to be held. She reminds Ash that he has to get registered for the Johto League, so she leads him to another room. Joy takes Ash's new Pokédex and slips it into a machine. After doing some typing, Joy is done. Ash, now eligible for the Johto League, thanks Joy as she gives him the Johto League Guide Book. Misty asks how many badges Ash needs to compete, and Joy tells her that he needs eight. She suggests that the best place to start is the first gym in Violet City. Excited, Ash swears that he'll catch up with Gary.
As Ash takes a look back at New Bark Town, he waves goodbye to Elm, Joy, and Jenny as he heads for his next big adventure. Elm tells Totodile that tomorrow he'll meet a new trainer and they'll become best friends just like Ash and Pikachu are. The gang walks away, with Jigglypuff in close pursuit.