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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 {{ga|Brendan}} or {{ga|May}} (whichever is the opposite gender as the player), the child of Professor Birch who will become one of the player's [[rival]]s. After the introduction, Brendan or May 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 {{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 Brendan or May on Route 103, they have their first {{pkmn|battle}}, after which they return to Birch's lab, where the player receives a [[Pokédex]] and some [[{{i|Poké Ball]]}}s. Outside of the lab, the player's mother gives them the [[Running Shoes]]. Once the player arrives in Petalburg City, they meet with their father at the Gym, where he tells them 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 to help him catch 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/3|Ru}} or [[Team Aqua]]{{sup/3|Sa}}. After battling, the grunt reveals that their team is after something in [[Rustboro City]].