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The player starts their journey in [[Littleroot Town]], where the family has just moved from the [[Johto]] region after the player's father, [[Norman]], became the leader of the [[Petalburg Gym]]. The story starts off with the player riding in the moving van, which arrives in Littleroot. After exiting the van, the player's mother explains that they have just arrived at their new home; they then enter the house together, and there are {{p|Machoke}} movers carrying boxes. The player's mother suggests that the player introduce themselves to [[Professor Birch]], a friend of Norman's.
Upon arriving at Birch's house, his wife greets the player, and upstairs the player meets May or Brendan (the alternate-gender player character of the player), the child of Professor Birch; after the introduction, she or he soon leaves to join Birch, who is out in the field. The player then finds Birch on {{rt|101|Hoenn}}, where he is being chased by a wild {{p|Poochyena}}. Birch asks the player to take a [[{{i|Poké Ball]]}} out of his bag, which is lying on the ground; the player then chooses between {{p|Treecko}}, {{p|Mudkip}}, and {{p|Torchic}} as their [[starter Pokémon]]. After choosing, a battle immediately begins with the wild Poochyena. After rescuing Birch, he lets the player keep the chosen Pokémon as thanks for saving him. He then tells the player to meet up with his kid on {{rt|103|Hoenn}} for pointers on how to be a Trainer.
Once the player finds May or Brendan on {{rt|103|Hoenn}}, they have their first trainer {{pkmn|battle}}, after which they return to Birch's lab, where the player receives a [[Pokédex]] and some [[Poké Ball]]sBalls. When leaving through Route 101, the player runs into May or Brendan who gives him a new upgrade for the [[PokéNav Plus]], the DexNav, and teaches him how to use it. Once the player arrives in Petalburg City, he meets with his father at the Gym, where he tells him that he is happy to learn that they have become a Trainer like him. During the conversation, a local boy named [[Wally]] enters the Gym and asks Norman's help for catching a Pokémon. Norman loans Wally a {{p|Zigzagoon}} and a Poké Ball. He then asks the player to go along and help Wally with his task. On {{rt|102|Hoenn}}, Wally catches a {{p|Ralts}}, and the Trainers then return to the Gym, where Wally gives his thanks before being called home by his mother. Norman then encourages the player to travel [[Hoenn]] and challenge the region's [[Gym Leader]]s: [[Roxanne]], [[Brawly]], [[Wattson]], [[Flannery]], [[Norman]], [[Winona]], [[Tate and Liza]], and [[Wallace]].
The player then travels through {{rt|104|Hoenn}} and [[Petalburg Woods]]; just before the exit from the woods, the player encounters the nefarious [[Team Magma]]{{sup/6|OR}} or [[Team Aqua]]{{sup/6|AS}}. After battling, the grunt reveals that their team is after something in [[Rustboro City]]. Upon exiting the forest, the player is spotted by a [[Zinnia|red-eyed grunt]] who reports to her leader.