Caterpie is first mentioned to the player and partner by his worried mother, Butterfree. She explains that a fissure opened in the ground and Caterpie fell into a cavern. She tried to rescue him herself since he is too young to get out alone, but some Pokémon started attacking her. Since she was too weak to continue, she asks the player and their partner to help, and the partner immediately accepts. The player and their partner find Caterpie crying at the end of Tiny Woods and reunite him with his mother. After the player and partner agree to form a Rescue Team, Caterpie expresses his wish to join when he grows up.
Later, Caterpie asks the player to save his friend, Metapod, who has gotten lost in Sinister Woods. Team Meanies overhears this and also decides to go and save Metapod, saying that if they do so, Caterpie will have to join their rescue team and that they will claim a reward from his mother. The player character and partner assure Caterpie that they will rescue Metapod first. They follow Team Meanies to Sinister Woods and defeat them. They then proceed to rescue Metapod, reuniting the two friends. After this, the two are often found near Whiscash Pond together.
After the player and partner defeat Rayquaza, Caterpie appears with everyone else on top of Hill of the Ancients to celebrate the victory. A few days later, he informs the player and partner that Snubbull has evolved.