It all begins in the core at the world of Pokemon in the swamp. The Mask of Life which rests at the bottom of the murky waters lights up with May's voice creating a new body and hovercraft from the dirt bursts from the swamp and flies to the skies of the cavern. Meanwhile in Kanto, Ash and his remaining friends see the Temple of the Sea still at the botttom of the sea. They knew May's near sacrafice saved Manaphy from death but the temple itself was still in danger. They are suddently caught in a flash of light and transported to the core of the Pokemon world (they don't know that yet). They find themselves standing on a staglidite, high up in the skies of the cavern roof. Suddently, Ash notices people with jet packs fleeing the rock while dodging dark lasers which one hits the roof and a giant shard of rock heads for the group. With nowhere to run, all seems lost. 5 mysterious Pokemon swoop in and just saves them. They take them to a carvern which they introduce themselves Tanma, Solek, Thotok, Mazeka and Galva. They then tell them that all the secrets of Pokemon will be found within the swamp of secrets far down to the bottom of their home, Karda Nui. Tanma then tells Max that he saw the Mask of Life fall to the swamp with someone using its energies. Max, realising these events tells Ash, Dawn and Misty to head for the swamp while he and Brock helps the villagers fight against mutant Pokemon Humans corrupting villagers and using them to conquer Karda Nui for Team Rocket. Both separate groups recieve equipment for their separate missions allowing them to fly across Karda Nui. Ash, Dawn and Misty fly down to the swamp not hearing or noticing May ascending to the villages. Brock and Max quickly come face to face with two figures called Vamprah and Chirox and have trouble using the new equipment to take them on. Just as they are in the line of fire with no escape, May suddently comes from behind and attacks the two mutants with the village resistance and Pokemon by her side. They eventually defeat the foes but the explosion knocks May off her jet board. Max flies up to catch her just as a loud boom sends a shard towards Brock. May uses the Mask of Life to create a copy from a pile of rocks and it sacrafices itself to save him. Brock then asks her not to scare him like that again. Max soon realising that Ash and the others were still in the swamp looking to unlock the secrets whilst the Mutant beasts were on their tail.
Swamp of Secrets
Brock, Max and May descend to the swamp to find Ash, Misty and Dawn under attack by 3 more mutant beasts adapted to the swamp and daring to attack any foe that enters it. Ash and Pikachu struggle under 4-legged Krika, Misty and Starmie under fire from swamp beast Gorast and Dawn and Piplup dealing with not one but 9 copies of Bitil. As Ash struggles to get an attack on one of Krika's 4 legs, May swoops in and knocks off one of the legs causing him to topple over. Just as Gorast is about to launch her ghost blaster, Max fires at it damaging it severly. She then retreats from the battle. Dawn starts to get dizzy as Bitil keeps on multiplying to one million copies. As all seems lost, Brock uses a trick of the light to make the Bitils attack themselves so that she could attack the real one. Bitil then retreats from the scene. Ash and the group regather in front of what he found. A giant dome with a inpenatrable barrier. He explains he gathered the keystones to shut down the field before Krika attacked. They enter the dome known as the Codrex without knowing Mutant Antroz following behind them. They come to a giant room with a mysterious painting of the Temple of the Sea. May is about to step forward when Antroz sends a dark beam knocking her into the painting. She suddently see visions of the past of a similar arduous journey set by six people of the sea before noticing the same thing she did to save Manaphy's life only like the Mask of Life said to her they were sacraficed being afraid of the consequences as it spared her life for her courage. There the visions end. A huge battle ensures between Ash, Dawn and Misty against all six mutants. Max, May and Brock run deeper into the Codrex out of the battle. They come across a strange mechanism used to keep the Temple of the Sea safe from intruders. May soon realises the mechanism was for her to use her spirit with the Mask of Life to awaken the Temple. She says one goodbye to Max and Brock before using the device to begin to awaken the temple. She then tells Brock and Max to stop the battle and get the rest of the group and villagers out of Karda Nui before an energy storm destroys everything from her actions. Max and Brock with the rest of the group begins to get all the villagers and Pokemon as the storm begins. They just get themselves out of Karda Nui before the Mutant's dying words "The temple is awakened, we have won."
The start of a New World Ordeal
The remaining group arrive in Kanto to see the Temple of the Sea rising as a mighty giant. Ash walks up to the shallow sea to look at the giant before hearing May's voice saying to him "Thank You".