In Ivysaur's Mysterious Tower!, Giovanni informed Team Rocket of a new secret weapon that he granted the trio access to. Pelipper delivered the Rocket Prize Master to them in Vermilion City, when they were confronted by Ash and Goh whilst they were trying to steal a group of Bulbasaur and Ivysaur.
In Kicking It from Here Into Tomorrow!, Pelipper was resting in Vermilion City when Goh came across it and attempted to catch it. This caused Pelipper to fly away, inadvertently leading Goh to discover Team Rocket's secret base.
Pelipper continued to deliver the Rocket Prize Machine to the trio whenever they request it.
In To Train, or Not to Train!, Pelipper was used in battle by James when the Rocket Prize Master did not deliver a Poké Ball to the trio. Initially, Pelipper managed to withstand Professor Cerise's Yamper's attacks, but it lost after Yamper teamed up with an Eevee.
As time went by, Pelipper got closer to Jessie, James, and Meowth, resting with the group in a calmer time. In A Rollicking Roll…, Pelipper tried to use the Rocket Prize Master while everyone was resting, due to a malfunction the equipment ended up releasing several Poké Balls containing several Gulpin.
In Errand Endurance!, Team Rocket sent Pelipper to get them some Casteliacones to go with their apple pie. With help from Team Rocket, Pelipper was able to collect some Casteliacones and returned to their base with them, only for Morpeko to eat them before they could.
Pelipper is dedicated to its job of delivering the Rocket Prize Master to Team Rocket at their request, no matter where they are. Pelipper is also capable of evading capture, such as when it flew off to avoid being caught by Goh in Kicking It from Here Into Tomorrow!. When the Prize Master malfunctions and no Pokémon are sent out, Pelipper voluntarily steps in to assist, as seen in To Train, or Not to Train!.
Pelipper is strong in battle, as seen in To Train, or Not to Train!, where it was even able to withstand a super-effective Spark from Professor Cerise's Yamper.
Pelipper is shown to be absent-minded, as seen in Errand Endurance!, when Team Rocket had to disguise themselves as ice cream vendors and give Pelipper the ice cream themselves when it forgot what it was supposed to be doing.