A little while after defeating Skarmory at Mt. Steel, Caterpie visits the player and asks them and their partner to go to Sinister Woods to rescue his friend Metapod, who has gotten lost there. Team Meanies overhears and decides to rescue him instead, demanding that when they do, Caterpie will have to join their Team and his mother will have to pay them a high fee. The player's team assures Caterpie that they will rescue Metapod first, so they follow Team Meanies to the dungeon and defeat them in battle. Afterwards, Metapod is reunited with his friend and expresses his gratitude to the player's Team.
Metapod later helps to build the player's new Team Base, using his silk to stick parts together. He then later appears on the Hill of the Ancients to celebrate the victory of the falling star being destroyed. After this, he and Caterpie can be found together at Whiscash Pond.
For more information on this Pokémon's species, see Metapod.