Pokemon are peculiar creatures with a vast array of different abilities and appearances; many people, known as Pokemon trainers, capture and train them, often with the intent of battling others. Young Satoshi has not only dreamed of becoming a Pokemon trainer but also a "Pokemon Master," and on the arrival of his 10th birthday, he finally has a chance to make that dream a reality. Unfortunately for him, all three Pokemon available to beginning trainers have already been claimed and only Pikachu, a rebellious Electric type Pokemon, remains. However, this chance encounter would mark the start of a lifelong friendship and an epic adventure! Setting off on a journey to become the very best, Satoshi and Pikachu travel across beautiful, sprawling regions with their friends Kasumi, a Water type trainer, and Takeshi, a Rock type trainer. But danger lurks around every corner. The infamous Team Rocket is always nearby, seeking to steal powerful Pokemon through nefarious schemes. It'll be up to Satoshi and his friends to thwart their efforts as he also strives to earn the eight Pokemon Gym Badges he'll need to challenge the Pokemon League, and eventually claim the title of Pokemon Master. [Written by MAL Rewrite]

Satoshi and his friends get lost in an unknown wasteland. They eventually come across a "Water Pokemon Show" performed by the star of the Mariner Troupe, Hiromi. Hiromi is a descendant of the troupe of Water People able to communicate with water pokemon, and she tells our heroes the legend that's been passed down by her people for generations. According to legend, a temple the Water People built called "The Water Temple Akuusha" rests somewhere in the ocean, and a treasure called "The Water Crown" is hidden there. It's said that no one has ever seen this treasure, but that changes when a Pokemon Ranger named Jack Walker (aka Jackie) appears to chase aftert it. Jackie is on a top secret mission that has him protecting the egg of the leader of the water pokemon, Manaphy. This pokemon, called the "Prince of the Sea," needs to be taken to the Water Temple Akuusha, so Satoshi-tachi and Hiromi decide to help him. Along the way, a pirate named Phantom attacks our heroes from his great submarine. Phantom plans to use the Water Crown's power to help him conquer the world, but he'll have to solve the mystery of Manaphy's egg first. When the Rocket-Dan get into the mix, Jackie uses his Capture Styler to borrow the power of a nearby pokemon to stand up to them. Satoshi and Pikachu enter the fray, but they still have to contend with the attacks of Phantom's powerful high tech mecha! Suddenly, the egg starts to shine with a vivid light, and Manpahy is born! What is the mystery of the legendary treasure? What mysterious powers does Manaphy have? Can Satoshi-tachi and Jackie complete their top secret mission? The journey to reach the Water Temple Akuusha has begun!

Mii Snowdon is left on her own after her father disappears while investigating the mysterious letter-shaped pokemon called the Unown. The only clue to her father's disappearance is a box containing several tiles. While playing with these tiles, Mii makes a wish to see her father again, and this wish awakens the Unown—who summon the lion-like, legendary pokemon Entei to act as her father. Meanwhile, Satoshi heads to Greenfield with his faithful pokemon companion, Pikachu, to meet with his friends, Kasumi and Takeshi. When they reach the area, they are shocked to find the place crystallized. They quickly learn that the Unown are responsible for this, and that they will need to be defeated in order to restore Greenfield to its former beauty. The situation becomes personal when Satoshi's mother is kidnapped by Entei. To discover why his mother was taken away, Satoshi, along with his friends and pokemon, must travel the crystallized landscape to confront Entei and the Unown. [Written by MAL Rewrite]