The game begins as always with you, the player, a teenager, in your home in Perido Town. Your mother - a retired master Pokémon trainer - calls you to the TV, where you see there is a commotion in the next town over, Citrelle. Supposedly there's a Pokémon battle happening in the middle of town between local trainers and a mysterious group who are ranting about saving the environment (W)/ranting about overcrowded cities (I).
Enter your friend Louis, who excitedly suggests that you go and check out the ruckus together - after all, the two of you want to become Pokémon trainers, so you should go and see how it's done. You travel to Citrelle Town together, and find that the battle is over, and the mysterious strangers have left. In the aftermath, they left behind a container filled with three unusual Pokéballs, containing the Pokémon Petaby, Bratoo and Findol. You and Louis each pick one, battle each other and return home. As you leave, a young woman approaches the container and takes the last Pokéball, talking quietly to herself.
You get home and show the Pokémon to your mother, who recognises the symbol on the Pokéball: It comes from the Spinele Pokémon Laboratory, run by an old friend of hers, Professor Hawthorn. She suggests that you and Louis take the Pokéballs to the Lab, but then recalls that the Lab is part of the Spinele Cty Institute, which only admits trainers who have earned three or more Farroh Gym Badges. She is about to head off to take them there herself, when Louis suggests that you and he instead use this as an excuse to begin your own Pokémon adventures.
And so you set off, soon splitting up. Via Citrelle Town you reach Spessar City, and cross the Iridescent Bridge to Malack City, where you challenge the first Gym Leaders, Iuan, in his water-type aquarium gym. With the first badge obtained, you can visit the capital city of Farroh, Carnelia, north of Spessar. The road there is still under some construction, the surrounding forest having recently been cut down.
Upon reaching this road, you find the same environmental activists who were on the TV in Citrelle Town trying to halt the construction of the road by threatening the roadworkers with their Pokémon. You bravely step in and challenge the leader of the group, who calls herself Dria, a "warrior of Team Gaia". (W)/you come across the group from the TV in Citrelle Town, who are hassling the roadworkers with their Pokémon, trying to make them work faster and more efficiently. You bravely step in and challenge the leader, who calls himself Etnus, a "Fighter of Team Metro". (I) When the group are defeated, they reluctantly vanish, and the roadworkers thank you and let you pass on to Carnelia City.
You enter the traditional southern bank of Carnelia City, with its old-fashioned buildings and bustling yet dignified inhabitants, far from the noise and fashion of the northern bank. You challenge Normal-type Gym Leader Lucinda at her museum, and then head towards Tormalos City, via Spessar and Malack. On the way you pass through the quiet, oddly lifeless Clinolor Town and visit its deep mines, which are surrounded by fables and legends of mythical Pokémon. When you get to the tree-filled Tormalos city, you challenge Grass- and Fire-type leader Frederick in the old foundry-turned gym.
When you try to head over to Spinele City to go to the insitute, Louis appears and says he tried the same thing, but wasn't allowed in since he didn't have a diploma in "Basic Pokémon Studies". He tells you he heard that you can obtain a diploma at the school in Quarta City, so you head through the mountains and stop at Lapiville Town on the way through the crystal-filled caves. Here, you encounter Team Gaia(W)/Metro(I) again, who are hoping to harness the supposed power of the crystals. You battle another member of the team, Nymo(W)/Amphia(I), who mention their leader, Artemia, who wants to stop the razing of Farroh's natural habitats and demolish the 'ugly' cities that pockmark its landscape to return the region to its original beauty(W)/Stephanus, whose aim is to fill the whole landmass of Farroh with one vast metropolis where Pokémon and people can live happily together, safe from overcrowding and the dangers of the wild.(I).
You move on to Quarta City and visit the Pokémon School there, completing some tests and defeating a few trainers to gain your Basic Pokémon Studies diploma. With that in hand, you and Louis make your way to Spinele City, which is almost entirely taken up by its prestigious Pokémon Institute, which you are admitted to with your three badges and diploma. You work your way through the institute until you are able to challenge your fourth gym-leader, Psychic master Huberta - the very same Professor Hawthorn that your mother sent you to find. Before you battle, you show her the Pokémon you found and explain the situation to her, and she takes you to her Lab to talk.
You and Louis explain all about Team Gaia(W)/Metro(I), who despite their well-meant aims are using overly violent methods to get there. The Professor understands, and thanks you and Louis for retrieving her Pokémon. She asks where the third one is, and the girl from earlier enters. She introduces herself as Polly, an amateur Pokémon researcher and journalist. She explains that she has been following you and Louis on your travels and observing how you raise your Pokémon, then reveals that she has been raising the third one you left behind. Professor Hawthorn notices the three of you are raising the Pokémon well, and suggests that you keep them and continue on your journeys, whilst keeping an eye on Team Gaia(W)/Metro(I). She then finally agrees to battle you, earning you your fourth gym badge.
