He is shrouded in mystery for most of the Battle Frontier saga. Unlike the other Frontier Brains, his silhouette is not shown on its own during the opening and is only seen in the center of the group shot. Trainers will only find out the location of the Battle Pyramid after they have collected the other six Symbols. This may mean that Brandon ranks higher than the rest of the Frontier Brains, although in the video games and manga, this position belongs to Anabel. When Ash finally gets his sixth Frontier Symbol in Second Time's the Charm!, he learns that it is located near Pewter City.

His first battle with Brandon occurred in Battling the Enemy Within!. At the time, however, Ash was possessed by an ancient king of the Pyramid who battled Brandon's Regirock with Ash's Sceptile. Sceptile was defeated, although Ash eventually regained control of his body, and the Pyramid was moved to an area near the Indigo Plateau.

For their second battle in Overjoyed!, Ash's Torkoal squared off against Brandon's Registeel. However, Torkoal was, like Sceptile, defeated by Brandon's Legendary Pokémon.

In Gathering the Gang of Four, Ash and co. met up with Brandon in a forest. In Pace - The Final Frontier!, Brandon and Ash fought in a 4 vs. 4 battle. Brandon's Dusclops defeated Ash's Charizard in the first round, but was then defeated by Ash's Bulbasaur. Then, Brandon's Ninjask squared off against Ash's Squirtle, where Squirtle was able to beat Ninjask with a Hydro Pump. In the next round, Squirtle was defeated by Brandon's Solrock, which in turn drew with Bulbasaur. With both competitors left to their last Pokémon, Ash used Pikachu while Brandon unveiled yet another Pokémon from his legendary collection: this time, a Regice. Despite the odds, however, Pikachu managed to hold its own against the legendary golem and came out victorious, becoming only the second Pokémon in the anime to have defeated a Legendary Pokémon, after Charizard.

Brandon appeared again in A Pyramiding Rage!, where he wanted to research the Snowpoint Temple. While meeting up with Ash and friends, he is challenged to a full battle by Paul. Paul loses the match easily due to him losing control of his emotions. Brandon later mentions that they would battle again when Paul is ready.

In Pillars of Friendship, Brandon tries, and fails, to stop Pokémon Hunter J from disturbing Regigigas in the Snowpoint Temple, which then goes on a rampage. It eventually calms down when Brandon saves it from being turned into a statue by J. Brandon then decides to stay at the Snowpoint Temple, not only to rebuild it, but also allow Regirock, Regice, and Registeel to become the new pillars that protect Regigigas.