Ash and a Schoolboy are having a Pokémon battle. When Chikorita gets tired, Ash decides to use Pikachu against the Schoolboy's Raticate. When he attempts to return Chikorita into her Poké Ball, Chikorita refuses and evades it. The Schoolboy's mother calls her son in for dinner, just as Ash is finally able to return Chikorita. Ash and his friends go to a Pokémon Center to eat, but Chikorita doesn't participate. Pikachu tries sharing his food with Chikorita, but she bats the plate away with her leaf. Observing this, a glasses-wearing Nurse Joy, who has a degree in Pokémon psychology from Celadon University, walks up and requests having a counseling session with Ash, Pikachu, and Chikorita. After Ash answers several questions, Nurse Joy deduces that Chikorita is jealous of Pikachu. She escorts the group to the Center's greenhouse, and suggests putting Chikorita together with plants for the night to make her feel comfortable.
During the night, Pikachu approaches Chikorita in the greenhouse. As Pikachu watches, Chikorita pops out of her Poké Ball and proceeds to leave the Center. Despite Pikachu's attempts to intervene, Chikorita manages to run off, pursued by Pikachu. She soon finds a warehouse to sleep in, but is awakened by four Fighting-type Pokémon: Machoke, Hitmonlee, Hitmonchan, and Primeape. Chikorita attempts to ignore the Pokémon, but Primeape attacks her. Chikorita soon defeats Primeape with a Vine Whip, shocking the other three and causing them to kneel out of respect for Chikorita.
The next morning, Nurse Joy shows Ash and his friends footage from last night, which reveals that Chikorita had run away. The group begins searching, and Ash sends out Bulbasaur at Brock's suggestion. Meanwhile, Team Rocket, who is spying nearby, sees Chikorita and Pikachu's disappearances as an opportunity to capture them. James contacts Meowth, who is in their hot-air balloon, to search for Pikachu and Chikorita. Meowth soon spots Pikachu, who is traveling through some long grass.
Pikachu heads inside the warehouse and finds Chikorita. She refuses to go with him when Jessie and James appear at the doorway and recite their motto. James casts a net, but Primeape knocks it back, and the other Fighting Pokémon appear. Meowth sends in a mecha constructed from old tires, which knocks the Fighting Pokémon away, and its rubber body makes Pikachu's Electric attacks useless. Pikachu and Chikorita are soon captured just as Ash and his friends arrive. Brock spots the mecha's antenna, which prompts Ash to send out Heracross. Heracross uses its large horn to send Ash up onto the machine, but the mecha dodges and Ash lands in a pile of tires. Ash then spots a nearby water tower, and rushes up a flight of stairs to get the same height as the mecha.
Ash jumps to reach the robot's antenna, but Meowth has the mecha move out the way and Ash is sent plummeting to the ground. However, Chikorita catches him with her vines, and with a bit of difficulty, she manages to hoist Ash up to the mecha's head. Ash yanks off the antenna dish, causing the mecha to go haywire, allowing Pikachu and Chikorita to be released. The robot grabs onto the ropes connected to the Meowth balloon, and in desperation, Meowth cuts them. Jessie and James, who were climbing the ropes, fall into the mecha's head, and Team Rocket is blasted off when it explodes. Afterwards, Chikorita decides to leave the warehouse, and the four Fighting-type Pokémon say goodbye to her.
Back at the Pokémon Center, Ash thanks Nurse Joy for diagnosing Chikorita's jealousy, which appears to have subsided for now. As they are about to head off, Pikachu jumps onto Ash's shoulder, and at Ash's insistence, Chikorita leaps onto the other.