If Brendan is selected as the player character, he starts his journey moving from his home in Johto to his new home in the town of Littleroot in Hoenn. After saving Professor Birch from a wild Pokémon, he is given one of the three starters of the Hoenn region. Brendan develops a close bond with May, and eventually Wally, who both act as his rivals. Brendan goes on to gather the eight Badges of Hoenn, stop the plans of Team AquaSEAS/Team MagmaREOR and conquer the Pokémon League all before going off to face the Battle FrontierE.
As a non-playable character
If Brendan is not selected as the player, he is helping his father Birch finish the Hoenn Pokédex and becoming a Pokémon Professor. He is also the player's rival and friend. Along with May (when playing as Brendan), they are the only rivals unavailable for battle after entering the Hall of Fame. Additionally, they both are the only ones to not evolve their starter Pokémon into its final form, except for in Omega Ruby and Alpha Sapphire, where their starters have been fully evolved by the battle that takes place after the credits.
If the player never uses the Rustboro City PokéCenter and blacks out or uses Teleport after rescuing Peeko, they will encounter Brendan on Route 104 when going to Mr. Briney's home.