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.

An ancient prophecy tells of a day when the titans of ice, lightning, and fire are disturbed. When this occurs, Lugia, the guardian of the sea, will rise up and restore harmony. Enchanted by the words of the prophecy, Gelardan, a Pokémon collector, sets out on his airship with a dreadful plan to capture Lugia by going after these three titans. After Gelardan makes his move, drastic climate change begins to take place, as terrible storms start popping up all over the globe. One such storm causes the ship carrying Pokémon trainers Satoshi, Kasumi, and Kenji to drift off course and land on Earthia Island. Upon arriving, Satoshi is told of the ancient prophecy, and of his destiny as the chosen one who will help Lugia restore balance to the world. With the fate of the world in his hands, Satoshi must summon the courage to face the chaos that threatens to tear everything apart and stop Gelardan.

It was a successful science experiment gone horribly wrong. When a team of scientists discovers the DNA of the ancient Pokémon Mew, they harnessed the potential within it in an attempt to create the ultimate living weapon. With advanced cloning techniques and resources provided to them by Team Rocket crime syndicate leader Giovanni, the scientists succeed in creating the powerful psychic Pokémon, Mewtwo.Pokemon: Mewtwo no Gyakushuu reveals the terrifying power of Mewtwo as he learns that not only was he created to be an experiment, but also to be a tool for Giovanni’s sinister dealings. Breaking free of his control, Mewtwo creates his own island fortress and reconstructs the cloning technology that gave life to him. Under the guise of being a master Pokémon trainer, Mewtwo lures the best trainers in the world to his base. Among these trainers are Ash Ketchum, his loyal Pokémon Pikachu, and their friends Brock and Misty. United together, human and Pokémon alike, they must not only discover the hidden secret of Mewtwo's plans, but stand against his terrifying might. If they fail, Mewtwo’s vengeance will not only lead to tyranny over all the Pokemon, but also the extinction of the human race.

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!