It all starts when Ash returns from the Isshu region to reunite with all his previous friends Brock, Dawn, Max, May and Misty. After a reunion party, all but May and Ash tuck in for the night. As the two watch the stars they notice one mysterious red star come in low, heading for the bay. May sets pursuit with Ash close behind. Suddently, a canister arises from the sea and the star strikes May at the same time, knocking her forward into the canister. The canister door shuts suddently and Ash sets chase with Staraptor with just enough speed to jump on to the roof. Hanging on tight for a day and a half, the canister reaches its destination on a mysterious island 600 miles south of Sinnoh. The door bursts open allowing Ash and Pikachu to enter to find May asleep. May wakes up suprised to find Ash inside and the door open. The two explore the beachside until the come across a strange person. Afraid at first, believing them to be invaders but after some explaining he tells them his story. A month ago, Team Rocket Elite members (Excluding Jessie, James and Meowth) that have mutated with their Pokemon are known as Piraka Pokemon. 6 of them invaded the island, Voya Nui, stolen a treasure called the Mask of Life and that they used it to mutate the inhabitants and most of the Pokemon that live there into strange, hideous, dark creatures that roam the island, destroying anyone under Giovanni's command. He then explains yesterday night that a red star would appear to someone with a strong connection to Manaphy (which immediatly sets flashbacks in May's memories) would come to save Voya Nui using the powers of the Pokemon masks, one for each of the six elements. The only two the stranger managed to save was the fire and electricity as the Team Rocket Piraka claimed the other 4. May puts on the fire mask and transforms into Combusken. The stranger explains that they can turn to their original forms by focusing their spirit which exactly what she does. He then shows them a bird Pokemon called Flyaliga, a rare evovled form of Flygon that can fly 1200 miles without being tired. Ash uses it to send a letter to Brock with the map to Voya Nui as he and May begin their journey.
Back in Kanto, Brock and the others were searching for Ash and May when the Flyalgia that Ash sent delivers the map to him along with letter. Brock decides that the map might lead to where they are. Dawn and the others decide to come and by studying the map she tells Brock before they start the journey its a possibility by an unknown island its a trap. Back on Voya Nui, Ash and May start by heading through the Ancient Forest to find the Air Mask only to end up facing Cassidie in her form known as Zaxtan. May takes the form of Combusken but all her attacks keep clashing with sand tornados created by Cassidie forming giant glass spires trapping her. Just as all seems lost, an earthquake pulls Cassidie underground, the glass spires shatter and Brock appears on his Onix with the Mask of Air. Ash then explains everything to Brock, Dawn, Max and Misty before May tells them of something bad which they need the Mask for that the Temple of the Sea is not only in danger again, it along with Manaphy is dying. They travel across the rest of Voya Nui, defeating Team Rocket Piraka through Icy Mountains, Undersea Caves, Team Rocket's Stone Fortress, Scorching Desert and The Voya Nui Volcano. They run into a few situations along the way but pushed on. With all 6 Team Rocket Piraka defeated, the group return to the shore to tell the stranger the good news. Happy of hearing it he introduces himself as Balta. After a victory party, Ash and May return to the beach to watch the stars at night once again. Despite defeating the Piraka, they still haven't found the Mask of Life and May begins to worry about Manaphy when a chill of evil breezes over them bringing them to a conclusion that the real evil hasn't been defeated. Balta and Dawn run down to them to tell them that a shadowy Piraka figure on a monstrous spider creature shrouded in shadow have kidnapped Max and Misty. Ash says that he and May must go after them before they get too far. Despite pleas from Balta, Dawn agrees for them to go. Balta eventually lets them go but warns them as he noticed the Piraka was holding the Mask of Life which means he can manipulate life forms in all ways. Back in the Underground Chamber, Max and Misty sit in a cage above a lave pit when the mysterious Piraka introduces himself to be Vezon and his mutated spider Pokemon Fenrauk. Just then the cavern wall blasts open revealing Ash and May in their mask forms. They decide to take on Vezon and Fenruak 2 on 2. They easily defeat the two but as the Mask of Life somehow had a mind of its own merges Vezon and Fenruak to form Kardas. Kardas begins his brutal assualt on the two but even with Ash merging all the masks gets defeated at the claws of the mighty dragon. Just as Kardas is about to destroy May, unexpectly Jessie, James and Meowth crash through the roof and take to the battle. Although they get defeated and blast off again, May pulls the Mask of Life from Kardas' back weakening him. Ash uses his chance to unleash an elemental blast at Kardas defeating him completley and freeing Max and Misty. Brock, Dawn and Balta come down to see Kardas drowning in the lava pit. May then begins to walk up the stairway to complete her task as the credits roll but not before at the end of the credits saying to be continued... .