Magmortar was first seen when it battled Maylene's Lucario in a flashback. Magmar won easily with its Fire Punch attack, earning Paul the Cobble Badge. Magmar was later used in Paul's battle with Brandon, fighting against Regirock, but quickly being recalled. He was sent out again to battle Registeel and hit it with its Flamethrower, but Registeel lands an Iron Head, which causes it to flinch. Unlike Paul's other Pokémon, who'd he give up on, he recalled Magmar. But, he had to recall it when his other Pokémon were beaten, he sent it out against Regirock. It blocks Flamethrower and defeats Magmar with Shock Wave.
Magmar evolved after fighting Brandon and as Magmortar and improved its strength. Magmortar was used in Paul's battle against Ash at Lake Valor, batting Pikachu. A Quick Attack lands, but Magmortar burns it using its Flame Body ability. After countering Thunderbolt with Flamethrower, Pikachu's finisher Volt Tackle is slowed by Rock Tomb, though Pikachu blocks Smog with his Counter Shield. Pikachu plants an Iron Tail, but substitutes him for Buizel due to the burn damage. Magmortar is able to continue after a direct hit from Aqua Jet and blocks Water Pulse with Rock Tomb. Buizel smashes through the rocks with Aqua Jet, but is crippled by Smog before Magmortar is recalled.
Magmortar was also used against Barry in the Sinnoh League where it easily defeated Barry's Skarmory with a single Flamethrower. It briefly faced off against Empoleon where it was shown to be strong enough to endure the most powerful Water type move, Hydro Cannon, but was recalled after being struck by the attack.
|Fire Spin||Lost Leader Strategy|
|Fire Punch||Lost Leader Strategy|
|Flamethrower +||A Pyramiding Rage!|
|Will-O-Wisp||A Pyramiding Rage!*|
|Rock Tomb +||Evolving Strategies!|
|Smog +||Evolving Strategies!|
|+ indicates this Pokémon used this move recently.*|
- indicates this Pokémon normally can't use this move.