Magmar 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. Paul later had his Magmar rest, and be taken cared of by three workers (who were Team Rocket in disguise).
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 caused it to flinch. Unlike Paul's other Pokémon, who'd he given up on, he recalled Magmar. But, he had to recall it when his other Pokémon were beaten, he sent it out against Regirock. It blocked Flamethrower and defeated Magmar with Shock Wave.
Magmortar was sent in Paul's battle against Ash at Lake Valor, batting Pikachu. Everyone became shocked, knowing this was Paul's Magmar that he had evolved. Pikachu's Quick Attack landed a hit, but Magmortar burned it using its Flame Body ability. After countering Thunderbolt with Flamethrower, Pikachu's finisher Volt Tackle was slowed by Rock Tomb, though Pikachu blocked Smog with his Thunderbolt-like Counter Shield. Pikachu planted an Iron Tail, but Ash substituted him for Buizel due to the burn damage. Magmortar was able to continue after a direct hit from Aqua Jet and blocked Water Pulse with Rock Tomb. Buizel smashed through the rocks with Aqua Jet, but was crippled by Smog before Magmortar was recalled.
As Ash was defeated, he remembered his battle with Paul's Magmortar. When Barry spoke how his father treated his Pokémon with respect, Ash remembered having faced Paul's Magmortar. It made Ash eventually realize that Paul was adapting his strategies on the experience he had acquired during his journey, like it was the case with Magmortar.
Magmortar was also used against Barry in the Sinnoh League. Barry's Skarmory used Spikes, but Magmortar defeated it with a single Flamethrower. It briefly faced off against Empoleon, enduring the latter's Hydro Cannon. He then swapped it with Ursaring, even if swapping his Pokémon would damage it by Skarmory's Spikes move.