Prior to A Difficult Parting, Foongy was one of the many Pokémon Team Plasma had liberated from people and planned to release into the wild after N's victory. When she was a Team Plasma Grunt, Whitley was presented with a group of liberated Pokémon, only to notice a Poké Ball among the group. Believing Poké Balls to be evil, Whitley attempted to remove the ball, only to discover that it was in fact a Foongus. Frightened, she threw the Foongus, only to apologize after discovering that he was actually a Pokémon. She then decided to give him the nickname Foongy, but Rood advised her not to do so as she would become attached to Foongy, making his eventual release into the wild a harder experience.
After Team Plasma was defeated, Whitley, her mother, and several other Team Plasma Grunts attempted to escape arrest by leaving N's Castle. Not wanting to leave N's friends behind, Whitley wanted to take the Pokémon with her, but her mother refused. After being allowed to pick the Pokémon she was closest towards by Anthea and Concordia, Whitley decided to take Foongy with her. Afterward Whitley and the others all made their escape from N's Castle.
Two years later Whitley is enrolled into the Aspertia CityTrainers' School by her mother. After arriving in class Whitley introduces herself and Foongy to her class. Later, Cheren has the students compete in a tournament battle with one side for the boys and the other for the girls. Together, Whitley and Foongy eventually win their side of the tournament, much to Whitley's annoyance as she wanted to avoid standing out. As a reward for winning, Whitley is given a Pokédex.
In Pokédex Lecture Whitley and Blake head to Pledge Grove to collect data for their Pokédexes. After Blake attempts to get too close to Whitley, Foongy quickly attacks with Sweet Scent to force Blake away. The Sweet Scent then attracts a wild Keldeo, which swiftly attacks the two Trainers, causing them to fall off a cliff. Blake manages to keep Whitley from falling, but was unable to do the same for Foongy. Whitley refuses to leave without the Mushroom Pokémon, and Blake goes down to save him. Reassuring Foongy that he does not want to cause harm to Whitley, Foongy allows Blake to help.
In Movie Panic, Foongy was Whitley's partner in the movie Foongus Girl at Pokéstar Studios. Despite the lines being scripted, Foongy participates in a real battle against Brycen-Man's Pawniard, taking it out with a Giga Drain. Before the battle can continue, a MechaTyranitar appears and begins attacking everyone in sight. Blake, in the guise of Dewott Kid, steps in to rescue Whitley while his Dewott defeats the Mecha Tyranitar.
Foongy is very protective of Whitley, quickly stepping in to help her when trouble comes up. Foongy is a powerful battler, easily winning the Aspertia CityTrainers' School tournament despite Whitley trying to lose. Blake was also impressed by Foongy's strength, making sure to be alert when around the Mushroom Pokémon. Foongy releases spores that can put people to sleep when frightened.