Flannery used her Magcargo in her batte against a trainer and his Trapinch, who challenged her. Magcargo used Flamethrower, which easily defeated Trapinch. Flannery teamed up with Tabitha to activate the Mt. Chimney volcano once more. Flannery's Magcargo used Flamethrower. Since it wasn't enough power, Tabitha gave Flannery some charcoal and had his Torkoal fire up the volcano as well. While relaxing in the hot springs, Flannery sent her Magcargo to battle Sapphire's Combusken, Chic. Both clashed for a while before Chic used Double Kick on Magcargo. Thus, Magcargo launched Flamethrower against Chic's Flamethrower. Chic, however, jumped and attempted to attack Magcargo, who emitted heat out of its shell.
The Gym Leaders and their Pokémon were recalled, including Flannery's Magcargo, for they had to fight Team Aqua and Team Magma's admins. Magcargo was seen again when Flannery ran along with it, as well as Wattson and his Manectric when they went to the south half of Hoenn. There, Manectric and Magcargo started attacking Kyogre. Magcargo continued attacking Kyogre before Flannery turned her attention towards Shelly, a Team Aqua admin.
|Flamethrower||Bubble Bubble Toil and Azumarill I|
|+ indicates this Pokémon used this move recently.*|
- indicates this Pokémon normally can't use this move.
- ^ RS032: Bubble Bubble Toil and Azumarill I
- ^ RS035: Assaulted by Pelipper II
- ^ RS036: Mixing It Up with Magcargo
- ^ RS042: Short Shift for Shiftry
- ^ RS055: The Beginning of the End with Kyogre & Groudon III
- ^ RS056: The Beginning of the End with Kyogre & Groudon IV
- ^ RS065: Bravo, Vibrava
- ^ RS066: Can I Ninjask You a Question?