Courtney first appeared in The Vision. She was initially seen guarding the Submarine Explorer 1 at the Team Magma Hideout, and stayed behind as Maxie(Pokemon Generation) and Tabitha left for the Seafloor Cavern. While alone, she experienced a vision of Primal Groudon attacking Team Magma, but this didn't deter her for long. She was last seen sending out her Camerupt to battle Brendan's Sceptile when he arrived.
Courtney plays a key role in the main story in Pokémon Ruby and its remake Pokémon Omega Ruby as an Admin to the main villainous team, Team Magma. Her appearances in the corresponding games Pokémon Sapphire and Pokémon Alpha Sapphire are limited to minor appearances, as Team Aqua are the main villains of these games.
In Pokémon Ruby, Courtney is first encountered at the Weather Institute attempting to steal the weather Pokémon. She later boards the submarine descending towards the Seafloor Cavern in order to awaken Groudon. She is battled by the player before Magma Leader Maxie. In Pokémon Sapphire, Aqua Admin Shelly fulfills the same role.
Due to the nature of Pokémon Emerald combining the stories of Pokémon Ruby and Pokémon Sapphire, Courtney isn't battled at all, as her role in Ruby is taken by Shelly. She only makes a brief non-talking cameo appearance alongside Maxie and Tabitha at the Seafloor Cavern after Archie awakens Kyogre.
In Pokémon Omega Ruby, Courtney sends a recon team, including Zinnia, to investigate and steal the Devon Parts for Team Magma; upon failing, the recon team warns her about the player. She eventually discovers the location of the Red Orb and informs Maxie, causing the him to cancel the operation at Mt. Chimney. Courtney is next seen at Southern Island, trying to steal Latios and the Latiosite for Team Magma, but is stopped by the player and Steven Stone, summoned by Latias to help. She later accompanies Maxie to Mt. Pyre, where they retrieve the Red Orb. When the player arrives and tries to stop them, Maxie has Courtney battle them while he departs to steal the Submarine Explorer 1 at Slateport City. When the player invades the Team Magma Hideout, Courtney once again battles them in order to buy time for Maxie to leave for Seafloor Cavern unobstructed. She later watches on as the harsh sunlight dispels upon Groudon's defeat or capture.
In the Delta Episode, Courtney plots to fulfill Maxie's crushed dream and takes matters into her own hands. She is encountered in Petalburg City harassing Wally, in the search for her own Key Stone. Wally insists that he does not have his Key Stone any more, as it was recently stolen by Zinnia. She then battles the player in an attempt to steal their Key Stone, and after the battle leaves for Meteor Falls. It is there whereupon she obtains her own Key Stone and with it launches an attack of the Mossdeep Space Center. She and a Team Magma Grunt battle in a Multi Battle with Steven Stone and the player, during which she shows her ability to Mega Evolve her Camerupt. After being stopped, Zinnia appears and Zinnia's Whismur steals Courtney's Key Stone.
In these games, Courtney is characterized by her bizarre speech patterns, which often involve pauses between words and speaking in a way that sounds robotic. She displays little to no emotion, but she looks up to Maxie. Courtney has high intelligence and was once a scientist. When she becomes interested in someone or something, she will not be deterred from it. Her role in Pokémon Omega Ruby is fulfilled in Pokémon Alpha Sapphire by Matt.