Prior to the start of her journey, Sapphire received Troppy from her father, Professor Birch, as a means for aerial travel. Troppy first appeared in the end of Bubble Bubble Toil and Azumarill II, as a way to quickly get up Mt. Chimney in order to chase Team Aqua. Upon reaching the top of the mountain, Sapphire spots Team Aqua's machine and has Troppy attack with Razor Leaf to scatter the Team Aqua Grunts below. Before they can attack the machine itself though Amber interferes with his Pelipper's Hydro Pump. As Troppy and Pelipper battle in the sky Shelly urges Professor Cozmo to set up the meteorite inside the machine as fast as possible. Flannery tells Sapphire to get past Amber and go for the machine, but Sapphire says she can't as Amber is feinting, pretending to fight badly and staying defensive, only attacking when they head for the machine in order to keep them at a distance. Unable to get in close range, Sapphire orders Troppy to use Magical Leaf, an attack that never misses. Unfortunately, it hits the machine just after Cozmo finishes setting up the meteorite, so the machine's defenses block the attack.
In Mixing It Up with Magcargo, Troppy battled Team Aqua. Sapphire has Troppy and Chic launch a barrage of attacks that continue to get countered, no matter how hard they try. Sapphire, suddenly realizing something, has Troppy and Chic hold their fire. Approaching the "enemy," Sapphire discovers that a ring of Mirror Coat has been set up around them, reflecting all their attacks back upon themselves, and that Team Aqua had left long ago.
In Master Class with Masquerain, Troppy, alongside Rono and Phado, were used in Sapphire's battle against Winona and her Masquerain, Swablu, and Beautifly. Although Winona's Pokémon proved tough, Sapphire manages to defeat her, earning the Feather Badge.
In The Beginning of the End with Kyogre & Groudon X, Troppy, alongside Ruby and Sapphire's other Pokémon, battled Archie and Maxie. Troppy was seen being pushed back by Archie's Walrein's Sheer Cold.
In Rayquaza Redemption II, Troppy flies Ruby into the final battle against Groudon and Kyogre.
In It All Ends Now VIII, Troppy battled alongside the rest of Sapphire and Ruby's Pokémon against Maxie and Archie.
In The Final Battle III, Troppy battled the Kyogre that Guile Hideout summoned.
In Omega Alpha Adventure 13, Troppy chased Zinnia after she goes to stop the rocket the scientists launched. After catching up, Troppy attacks with Leaf Tornado. Once landing on the rocket, he and Sapphire are attacked by Zinnia's Salamence, knocking them off and sending them into the ocean.