In Emerald, the protagonist moves to Littleroot Town of the Hoenn region from Johto. Upon rescuing Professor Birch from a wild Zigzagoon, he or she receives the Pokémon the player used to fight the Zigzagoon (either a Treecko, a Torchic or a Mudkip) and begins a journey. Like the previous games, the player's goal is to collect eight Gym Leader badges so he or she can challenge the Elite Four and become the Pokémon Champion. In these games, the rival is of the opposite gender and is more of a friendly helper, checking the player's progress at various times and giving items to help the player advance through the game.


The protagonist's father, Norman, is the Gym Leader of Petalburg City. The player will meet him in the city's Gym. Shortly afterwards, a young boy named Wally enters, who wants to catch his first Pokémon before he has to move away from Petalburg. The player accompanies him out into wild grass, where he catches his first Ralts. Wally is overjoyed and thanks the player. Later on, the protagonist faces him again in Mauville City, where he is seeking to challenge the Gym Leader there. After the player defeats him (or if he defeats the player), he reconsiders and decides to improve his team.


Every so often, the player runs into a man named Scott. Scott is a man looking for a strong Pokémon trainer. The player first encounters him in Petalburg City where he thinks the player might not be strong enough. After that, he starts to recognize the player's strengths and abilities.


The main antagonists that the player faces are Team Magma and Team Aqua. Emerald is different in that both teams are the villains in this game: in Ruby and Sapphire, one team was the antagonist and the other was the protagonist, trying to stop the other team. In this game, both teams are the antagonists. Instead of one team awakening a legendary Pokémon, both teams succeed in awakening a legendary Pokémon each. Team Magma's hideout is located at the base of Mount Chimney and is also the location where they awaken the legendary Pokémon Groudon. Team Aqua's hideout is east of Lilycove City, and they awaken the legendary Pokémon Kyogre at the bottom of the sea. The two Pokémon do not obey either team and begin fighting at Sootopolis City, and the weather alternates between sunshine and rain. The player must awaken the legendary Pokémon Rayquaza at the Sky Pillar, after which Rayquaza will swoop down and force the two combatants to stop, returning Hoenn to normal.


After the player acquires the eight badges, he or she is given entry to Victory Road, a location with high-level Pokémon and experienced trainers. The Pokémon League and the Elite Four are stationed in an area north of Victory Road. Near the beginning of Victory Road, Wally catches up to the player and demands another battle. His team has improved and after the player defeats him he vows to retrain until he triumphs. After defeating the Elite Four, the player may battle him again.


Once the player defeats the Elite Four, Norman gives the player the S.S Ticket for the S.S Tidal at the player's house. A news bulletin appears and it says a colored Pokémon is in flight through Hoenn. When the player's mother asks the player what color the Pokémon was, the player has a choice of the running legendary Pokémon (Red for Latias and Blue for Latios). A little later, the player receives a phone call from Scott whereupon the player will be allowed to enter the Battle Frontier through the S.S Tidal, where more Pokémon and more battles await.


Information from Wikipedia.

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