A mysterious Egg floats by in the ocean teeming with Pokémon. It glides along the water, going through a school of Remoraid, past a few ClamperlCloyster, and whatnot. The Egg finally settles down as a group of Lanturn and Chinchou have a look. Suddenly the school of fish-like Pokémon swim away as spotlights shine upon the Egg. Above the water, three helicopters hover low over the surface, scanning the Egg. Confirmation of the "treasure" is relayed to a large submarine underwater; where aboard Captain Phantom of the Phantom Troop executes his plan to secure the Egg. His Chatot flies onto the shoulder of the Captain's right-hand man, squawking the Captain's words.
Once the submarine gets close enough, a mechanical arm goes out to encase the Egg in a glass case and brings it back. With the operation a success, Captain Phantom heads down to the room where the Egg sits on a stand, still encased by the glass container. He marvels at his prize, and just before he could grab it, one of his pirates snatches it. Angered by the traitor, the Captain sends his men after him, but the mysterious traitor dodges their lunges, also correcting the Captain by revealing that he wasn't actually aligned with Phantom to begin with and thus wasn't actually a traitor. Escaping down a corridor, he is sandwiched at either end. Fortunately, there is a ladder on a vertical conveyor that he uses to escape. Getting to a higher floor, he jumps off the ladder, kicking the guardrail so that his pursuers can't find a way up without bumping their head on it. He makes a quick stop to the mess hall kitchen. While securing the Egg in a carrying bag, he makes contact with his "mission coordinator",Judy, to tell her he's secured the Egg. But just as he was ending the transmission, the pirates found him and began surrounding him. The man makes his move by jumping on pots, landing in a way that they fly onto the heads of the others as he makes his escape. On his way out, he pours a sack of potatoes onto the floor to keep the ones behind him busy.
Finding his way outside, the mystery man finds himself yet again chased down by the persistent crew of the submarine. He runs to the other side of the sub, jumping over a trapdoor that was opening to reveal Captain Phantom. The man reaches the bow of the submarine, finding himself trapped. The Captain releases a Pinsir and a Parasect and demands his name and threatens him to return the Egg, otherwise his Pokémon will attack. The man introduces himself as Jack "Jackie" Walker. He jumps up to the roof of the front part of the sub, just barely avoiding Pinsir's attack. At the very edge of the boat, he finds a few Mantine swimming about, feeling lucky they followed. Pulling out a Capture Styler, he manages to catch a Mantine just before Captain Phantom makes his way on top. Phantom threatens Jackie to return the Egg shortly before Jackie jumps off the boat, landing on the Mantine and escapes with it using Confuse Ray before diving into the ocean. Angry, Phantom tells Pinsir to use a Hyper Beam at the water, but by the time, Jackie swims off with the captured Mantine to safety. Pinsir and Parasect are obviously dazed, and Chatot is flying in circles. Nonetheless, Phantom deduces Walker's ties to the Pokémon Ranger organization with bemusement.

Main Storyline

AshBrockMay, and Max are traveling down a bright road. It's very hot and everyone is sweaty, tired, and desperate to find shelter. But where they're traveling on is nothing more than a dirt road with an expansive grass field and just a tree here and there and Max's PokéNav can't get a signal from their current location. Max stops to ask May for some water as he ran out. May gives her thermos to Max, who finds out that it's empty as well. Both collapse in shock while Ash looks back. He sees a ball of water floating in the distance, and is a bit confused before he mentions "Water". Max and May both perk up to see before Max begins running off towards where the water ball's direction.
They come across what appears to be several water balls, with Water-type Pokémon in them, and in the middle of it all stands a female teenager. Max goes up to her and asks if he can have some water, to which she gives permission. Max then goes to a nearby water ball and begins sucking some water from it, but a Gorebyss pokes Max away. The rest of the gang comes by, and the teenager asks who they are. Ash and his friends introduce themselves, except Brock who takes a good look at her and finally declares out that the teenager is Lizabeth. Brock then gets his little book of women he admires out and then pulls up Lizabeth's page. He explains that Lizabeth and her family run an outside circus show with water Pokémon. Pikachu wanders off a bit to find a Meditite and Medicham duo with a couple of Poliwag and a Poliwhirl. They greet Pikachu with the water Pokémon shooting some water out while the Meditite and Medicham use Psychic to form it into a Pikachu-shaped figure. The gang understands how the water balls are formed.
Several people soon come out of the trailer, wondering who Ash and company were. Lizabeth says that they're acquaintances and are just looking for some water. They all introduce themselves, the family of performers that runs the circus. The mother is Meredith, the father is Kyle, and the grandfather is Ship. They also have a clown who just joined them recently. May comments on how young Meredith looks, thinking she was Lizabeth's older sister. Meredith laughs and accidentally smacks May on her head a little too hard as she does.
Inside the trailer, Max enjoys a glass of water he needed. Afterward, a friendly Buizel comes by to play with him for a bit. As the others discuss things, May notices the Buizel hopping up to a bunk bed, going up to the top bunk where a canister lays. It presses a button and it clears up, revealing the mysterious Egg from before. May stares at it for a while before Kyle comes by and closes the curtain that was partially covering the bunk before excusing himself. To lighten up the mood, Lizabeth invites everyone to a free show they'll be performing in the next town. Everyone is happy to accept.
The show starts off with one large sphere of water being created, as a Seaking and Dewgong are let inside. Then the Meditite and Medicham then split the sphere into two, and soon Kyle and Meredith join in the act by diving in. Several more spheres are created with an assortment of Water Pokémon getting inside them. Lizabeth jumps in and rides the Dewgong to the top, clearing out and then jumping back in. Meanwhile, the clown walks around, wearing a Sharpedo get-up. As he's juggling a few balls, a group of Goldeen in small water spheres come near him. He uses the Sharpedo costume to "eat" the Goldeen, but then acts out as if he has indigestion and the Goldeen pop out on the other side. The gang was watching from the trailer nearby, and soon they were pushed into water spheres of their own, with everything combining into one. Then the Meditite and Medicham began surrounding the large water sphere with energy, before it exploded into steam, with the performing family and the gang at the bottom, and all the water Pokémon in their own bubbles, ending the show.
The Buizel was busy in the trailer, finding his way up to the bunk with the container. He takes a look at it again before it tips it over the edge. Grabbing it, he also tries to save himself before falling over onto the floor. He carries the container between the trailer and the circus-style decorated vehicle up front. May happens to be there when she spots Buizel, and sees the container once again. Up on the rooftops however, are JessieJames, and Meowth of Team Rocket, spying on what the gang and the circus troupe were up to. James happens to notice the container only for a split moment until the clown comes by to take it away from Buizel, and then leaves without a word, giving it to Lizabeth who then puts it upon a shelf, and closes a curtain around it. Later as the troupe was packing, the gang was invited to travel with them to the next town.
Meanwhile, Jessie, James, and Meowth relax at a fountain, when Jessie and Meowth notice James looking at a "Team Rocket Magazine". James mentions he saw the circus crew having an object he found in the magazine. And then he finds the page with a picture of the Egg and Captain Phantom. They plan on following the trailer, and will eventually make their attack. After the troupe packs up, the gang is invited to ride along until the next town, since it's a mountainous region. They take the offer and are soon off. As they pass by, the Team Rocket trio hides out in an alley. James is attempting to make a call, but had to cut the line when they realize they can just hitchhike on the troupe's trailer.
That night, while everyone was asleep, Buizel walked about the trailer, finding the shelf where the container was. He climbed up and presses the button, revealing the Egg once again. Moonlight shines through it and it begins to glow red. The light shines upon May, which creates dream of her being in an undersea world. Numerous water Pokémon swim by her before a mysterious one suddenly swims up to her. It was small, and looked very friendly and playful. Then up ahead, May could see what looked like an underwater palace surrounded by a bubble. The mysterious Pokémon soon swims past her and she screams out "Wait!". At that moment, she wakes up and also screams "Wait!". Lizabeth is sitting nearby wondering what happened before telling her good morning.
The trailer has stopped at a nearby river in a mountainous region, stopping for a late breakfast. A table is set up outside near the river and they enjoy their meal of Italian dishes. During the meal May talks about her mysterious dream last night, mentioning seeing a Pokémon she never saw before and a strange palace under the sea. Mysterious as it sounded to Ash and the others, the circus crew seemed to act out as if it was mysterious too, that is until Lizabeth and Minamo said that they had the same dream, and it's related to a legend, but Ship tells them to not tell right now. As they begin packing up after the meal, Jessie, James, and Meowth make their move. Jessie successfully finds the Egg after looking around in the trailer. But as they gather to get a closer look, the Egg begins to glow. A red lightning trails out and passes through each of their heads. When the odd experience ends, the group finds themselves have their body swapped, with Jessie as Meowth, Meowth as James and James as Jessie.
They continue to freak out about the swapping of minds until everyone comes back from their meal. They spot the Team Rocket members just as they leave. They begin to recite their motto, but end with a feeling that it doesn't feel right since their bodies are switched. They make a run for it with the Egg with Ash following them. But before Ash can reach them, they escape to a balloon, with a cycle driven propeller. They make their get away and Ash was about to have Pikachu take them down with Thunderbolt, but the clown suddenly comes up telling him to stop. If the balloon blows up, it'll damage the Egg. He takes out a Capture Styler from his pocket and finds a nearby Fearow. He uses it to catch the Fearow to pursue Team Rocket. Just as Fearow takes off, Pikachu hops on Fearow's back and the two Pokémon soon catch up. Pikachu lands on the cycling mechanism in front and begins sparking up. Then it snags the Egg and drops down, landing on Fearow. The bird Pokémon then flies up, threatening to poke the balloon as the Rockets panic, wanting the James Meowth to do something but he can't, and the Fearow pecks at the balloon, sending the Rockets away.
Fearow delivers Pikachu back to Ash, with May, Max, Brock, and Lizabeth nearby. Lizabeth takes the case with the Egg away before the clown shows up. Ash recognized the Capture Styler he used, and concludes he must be a Pokémon Ranger. The clown nods before taking off his disguise to reveal that was Jackie. Jackie shows the gang the Egg when things finally settle down, but his cover was compromised, as Team Rocket figured out about the Egg. But just as they were about to head back, several helicopters begin to show up on the horizon. And upon closer inspection, those helicopters bore the Phantom Troop's insignia. Jackie warns them of who they are and begins to make a run for it in a rocky path. Captain Phantom releases two Beedrill to chase after them, and soon the gang is making an attempt to run. They split up in order to split their pursuers up, with Ash following Jackie, and Max, May, Brock, and Lizabeth taking another route. Along the path Ash and Jackie take, Captain Phantom jumps down from his chopper and proceeds to chase after them. At some point, Jackie covers the Egg container with a towel and along with Ash, goes behind a rock just before the Captain could make it. Jackie is seen running off with the towel, and the Captain begins chasing after him. But Ash sneaks off in the other direction with the Egg.
Meanwhile Max and May split up from Brock and Lizabeth. Eventually Max and May cross paths with Ash, only to find that the Captain's right hand man was right behind them with a Beedrill. The Beedrill attacks with Pin Missile, Pikachu countering with Thunderbolt. Then the three try to escape, but Beedrill uses Sludge Bomb to block their path. Ash decides to stay behind to take care of the Beedrill, while May and Max run off with the Egg. Meanwhile, Captain Phantom manages to catch up with Jackie, only to have Jackie reveal that what he was carrying was a pair of juggling balls. He throws one at Phantom, in which he smacks it towards a nearby cliff wall. The ball simply bounces back and smacks Phantom in his face. Taking advantage of the odd but fortunate turn of things, Jackie runs off, jumping on a boulder. But somehow Phantom begins picking it up, and tosses it. Jackie jumps off however, but the Captain isn't interested in him anymore and begins searching for the Egg.
Max and May find themselves at split in their path, hoping that everyone is okay. Suddenly the Captain appears from behind and tries to pry the Egg container from May's hands. As May struggles to keep a grip, Max jumps on Phantom, stretching out his mouth. But Phantom was pulling on the lid, and soon it popped off, sending the Egg flying. May drops the container and dives in to catch the Egg. Ash manages to catch up at this point, but the Egg begins to shine. Then the entire Egg glows white before two antennae come out, and when the glow fades away, Manaphy is finally born. It opens its eyes to see May, but begins crying. May tries to calm the newly born Manaphy while the Captain is disappointed that something like Manaphy was the treasure he was looking for. But even so, he's not about to give up that easily and begins to make his move. Jackie comes in time to keep Phantom busy enough for Ash, May, and Max to escape. Jackie follows shortly afterwards and the four find the trailer (which Brock and Lizabeth managed to get back to beforehand). Jackie stays behind as the others get on to ambush Phantom to delay him once more.
The trailer takes off, leaving everyone to wonder about Manaphy. It slept in May's lap, happy and peacefully. Meredith wanted to try holding it, but as soon as she held it, Manaphy began crying. After Meredith gave Manaphy back to May, it stopped crying and was happy once again. They begin to wonder if Manaphy has imprinted May as its mother, considering that it was the first thing it saw. However, Phantom is once more on their tail, and two helicopters launch grappling rods to keep themselves affixed, and also to slow the trailer down. Ship comes in from the front car, telling the others inside to get in. Meredith first goes in; helping May so she doesn't fall. Brock then steps out to help Lizabeth, followed by Max and Ash. Ship gets out last as he unlatches the trailer. This sends the helicopters flying backwards, momentarily losing control as the trailer careens off a cliff. The choppers manage to cut their grappling lines and regain control.
Meanwhile, Jessie, James, and Meowth wake up from after crashing. They find themselves on top of a ruin. Jessie mentions having a weird "dream" that she was Meowth; the Meowth mentions that he was James, and James mentions he was Jessie. They suddenly realize that it wasn't a dream and that Pokémon Egg must've done something. The find Wobbuffet and Mime Jr. standing on the edge, "agreeing" with the weird occurrences that happened. But they soon see the circus crew pulling up to the ruin. After everyone gets out, the Phantom Troop soon arrives. Jessie, James, and Meowth decide to try to get Phantom to "recruit" them so that they can let Phantom do all the work in getting the Egg, and they'll steal it at an opportune time.
The gang heads down into to ruins, deeper until they reach what appears to be a dead end. Ship however holds his bracelet of seashells near a gem in the end wall. It glows to resemble a combination lock. He slides it to the right combination and a door opens up. Kai asks everyone if they have water Pokémon, since they'll be traveling down a canal. A few minutes later, Phantom steps down into the ruins, coming across the same dead end. However Phantom knows of this somehow and he pulls out a similar bracelet from his pocket. To his disappointment however, he comes across the canal, but there's no way for him to go. Getting back to the surface, Phantom finds the Rocket Trio washing his helicopter. After asking what they were doing and wanted, Jessie, James, and Meowth offer their cleaning services to Phantom, to which he promptly refuses. However, with stubbornness, the Rockets get to go along with Phantom as cleaners.
As the gang swims down the canal, Manaphy is enjoying its time in the water. They soon come up to another wall, in which is decorated with murals that tell a legend. Ship explains that there was once Ocean Temple named Samiya where water Pokémon and "people of water" had resided, and where a "King of the Sea" lived. However, evil spirits began invading, and so the king used his power to protect the temple, he encased it in a bubble and took it below the ocean. However normally it cannot be seen, but when its time for the "Prince of the Sea" to return, the moon will glow red for a brief period and Samiya will be visible. But there's a time limit once the Prince is born to return. Manaphy is this "Prince of the Sea", and so Ship plans on leading them to a port town, where he'll have a boat waiting to take Manaphy to Samiya.
Meanwhile, Phantom tries to find a possible idea to where the gang could've gone. But as his right hand man attempts to map out the route, the canal suddenly branches off into many different paths. They'll just have to spend their time finding out where they've gone.
The gang reaches a port town, where they wait for a while as Ship's boat comes along. They take a moment to rest and enjoy ice cream. Manaphy is now asleep in a bassinet, probably tired after all the swimming. Ship quickly finishes his cone as he spots his ship coming in, and warns the others that it's arrived. At the port, three of Ship's old shipmates GabuDabu, and Sabu step out to greet their old friend, and they want to go with Ship on the expedition to Samiya (though he doesn't tell them that specifically). Ship of course introduces the gang to his old shipmates, as he used to be an avid adventurer of the seas in his boat Blue Lagoon. However, Ship only takes his family, Jackie, and Manaphy along. May is upset at this, but she knows that it's for the better that Manaphy gets released. Gabu, Dabu, and Zabu though encourage May to stop them so she could get on, and Ash, not willing to put off an adventure like this, also joins in with May to stop the boat.
Manaphy on board soon wakes up and Jackie tries to comfort it. But it soon shoots out a red lighting that hits Jackie, and then trails down into the ocean back to the port. It travels towards Ash and May, and then suddenly Ash gets his foot caught by the lightning. Then, Jackie and Ash switch bodies, leaving them confused. Manaphy is happy though to see the Jackie Ash, but the real Jackie continues running towards the end of the port.
Later on, the gang gets on the boat, Jackie and Ash exchanging comments about that weird experience they just had. Jackie however says that this is one of Manaphy's powers, Heart Swap. Ship then tells May that Manaphy is referred to as the Prince of the Sea. May asks Manaphy if the reason he switched Ash and Jackie was so they wouldn't leave without her. Manaphy nods happily while May gives him a nuzzle on the cheek, saying he makes her happy. Manaphy then says happy, leaving everyone to the excitement that Manaphy can talk. Meredith recalls Lizabeth's first word which was apparently "Fu Fu," meaning food. Ship then says she loved to eat and Meredith chuckles. Ash and Max try to get Manaphy to say their names, but Manaphy resumes speaking out its name. Manaphy then rubs his flipper on May's cheek and she hugs it, saying that its cute. Jackie looks at them bonding, obviously not pleased about Manaphy getting close to May. Ship says that Manaphy needs to guide them to Samiya, and that Manaphy has to be released into the water. May lets Manaphy back into the ocean, and it jumps around swimming freely.
As Manaphy swims by, Ship brings the gang down to a lower part of the boat. After releasing a hatch, a dome in front of them opens up to reveal an underwater forward observation room. And they see Manaphy swim by with the various ocean faring Pokémon. Manaphy sees May and tries to swim up to her, but it hits hard on the glass dome. It begins crying but May tries to comfort it and Manaphy is once more a happy camper. Days pass, Manaphy still following the Blue Lagoon, trying to call out to May every so often. Jackie still sees some disproving in this, as if Manaphy gets too close to May, he may not go back to Samiya. Jackie though is scouting out of the ocean, probably looking for both the location of where Samiya is or perhaps looking out for Phantom. In one instance, he was parasailing to get a much better view. Ash watched him from below, commenting how cool it must be to be a Pokémon Ranger.
The boat makes a stop over a coral reef and the gang decides to take a swim. Although May seems still a bit preoccupied on the boat still, with Manaphy sleeping in her arms. Ash gets back on the boat to find Jackie, who hands him a towel as he comes up. Ash asks Jackie how he would decide to become a Pokémon Ranger. When Jackie was much younger, he got caught in a blizzard in his homeland. He found refuge in a cave, stumbling in and shivering from the cold. A Swablu comes down next to him, and he realizes that the cave is filled with Swablu, AltariaSentret, and Furret. They all huddle next to him to keep warm, and he stays the night there. The next morning, the storm has cleared up and all the Pokémon begin moving out of the cave. After seeing the flock of bird Pokémon take off, he was interested in Pokémon life, and wanted to defend such, and so he's been on adventures. After hearing that story, Ash gets a bit excited and he soon jumps back into the ocean, with Buizel. May goes in as well with Manaphy, and the both of them explore the coral reef together. They both resurface and May cuddles Manaphy lovingly.
Later that night, May is sleeping outside with Manaphy on a hammock. She tells Manaphy that she loves him, and asks Manaphy if he can say "I love you." Manaphy looks at her with a questioned look on his face. May then helps him out by saying "you." Manaphy almost said it, so May repeats "you" one more time. Manaphy finally learns and says "looove you!" May praises Manaphy, and Manaphy says happy. May affectionately hugs Manaphy while Manaphy tells May he loves her. Jackie is watching from above, and is very concerned about the relationship between Manaphy and May.
Later the next day, Brock is cooking a meal with Meredith, who finds his cooking to be very impressive. May is seen walking down the hallway towards the underwater observation when she hears Jackie talking with Ash. He tells Ash that Manaphy being all cuddly with May isn't such a good thing. After all, Manaphy is supposed to be the Prince of the Sea, a leader. How's a leader going to look if it acts how it does to May? At that, May suddenly comes in, telling Jackie that Manaphy will still do a fine job being a leader, and then she rushes out just as Lizabeth was about to enter. Manaphy is outside the boat, trying to get May's attention as May is curled up against a hallway wall. Lizabeth finds her and tries to console her, as May doesn't seem to want to let Manaphy go. To help her feel better, Lizabeth gives May her sea shell bracelet. Later that night, Manaphy sits on a rock, looking at the moon. It begins to sing, and as it does, Pokémon begin crowding near Manaphy. It seems Manaphy has influence on the Pokémon and perhaps its relationship with May hasn't hindered its position.
The next day, the boat comes to a stop at a crescent shaped island. Ash says that its time for Manaphy to eat. Manaphy jumps out of the water, and began looking around calling for May, for Manaphy really missed her and wanted to play with her. Ash decides to lighten up the mood by releasing his Pokémon out to play. Manaphy begins playing with Ash's Pokémon and begins playing a chasing game with Corphish. Feeling much better after yesterday, May begins putting on her bandanna, but it gets caught in a breeze and flies off into the ocean. Manaphy sees this and begins swimming after it as the bandanna gets caught on a Sharpedo, before falling onto a Relicanth. Above the surface, Corphish is still having a blast dancing in the small bay of the island before realizing everyone is back on the ship. It's already evening and everyone notices that Manaphy isn't back yet. Getting worried that something happened; Ship reveals another surprise of the Blue Lagoon. Towards the back at the bottom deck was a submarine bay. It's tethered to the boat for communication. Meredith takes the gang into the sub as Kai, Meredith, Ship, and Jackie stay behind to watch their progress. Corphish is left behind as well, due to not making it back to the boat before the group's departure.
Meanwhile in the distance, Captain Phantom has tracked down the location of the Blue Lagoon, and decides to play the waiting game. He'll simply wait for Jackie or the others to reveal where Samiya is, and then he'll make his move. Jessie, James, and Meowth, who are scrubbing the floor behind the Captain, begin confirming their plot on capturing Manaphy as well, waiting for the Captain to go into Samiya.
Meanwhile Manaphy explorers a crevice on the ocean bottom, passing by a Cloyster that has May's bandanna. But Manaphy goes a little too far out, and runs into a rough current stream before retreating back to the crevice. Manaphy notices the Bandana on its way back and the Cloyster opens up to let Manaphy take it. It hugs the bandanna for a moment before swimming back towards where the boat would be. May begins to worry that Manaphy either went away for good, or got lost. But just then, Manaphy appears outside the window of the submarine holding her bandanna. May asks Manaphy if that was what he was looking for. Manaphy affectionately cuddles the bandanna saying that it loves May. May leans up against the glass of the window saying that she loves Manaphy too. As they begin to go back though, they hit a high speed current that Manaphy ran into and lose control of the sub. The tether to the Blue Lagoon snaps and they disappear out of the Blue Lagoon's sonar. For a while, Lizabeth struggles with the controls until they see Manaphy swimming off as if wanting them to follow. Lizabeth follows Manaphy and soon afterwards, they come out of the current, but Manaphy still leads them off somewhere.
The Blue Lagoon spots the sub on sonar once again and they begin to follow it. However they notice another sub tailing them. Behind the Blue Lagoon's submarine is a smaller one belonging to Phantom. At some point, the Blue Lagoon's submarine blips out of sonar again. Underwater, it appears that it went through some kind of barrier. And then, the moon begins to transition into a red color. Soon, the water temple of Samiya appears right in front of the Blue Lagoon's submarine, with Manaphy still wanting them to follow. They find a "port" where they dock at. It appears that Samiya is encased in a bubble, with half of it full of water and is a complete water palace. Jackie fears however that the follower of the Blue Lagoon's sub is Phantom, and he dives in, capturing a Mantyke along the way to speed the process of getting down to Samiya.
As Manaphy leads the gang down a corridor, which is blocked by a waterfall. Manaphy steps up and begins to sing once more, with the temple repeating the notes in a lower tone. Then, the waterfall splits, and several more behind it split as well, opening the pathway deeper into the temple. Just then, Phantom docks at Samiya, making a little dance as he's found the temple. As he dashes onward, a pod connected at the back of the sub suddenly opens to reveal Jessie, James, and Meowth who snuck on to follow Phantom. The gang reaches what appears to be a dead end, but there's a small obelisk with some ancient writing on it. Meredith says that Ship can read it, and maybe they could go onward if he was here. Just then, Phantom makes his appearance, boasting that he could read it. It read that beyond is a treasure room of those who lived here had slept. He takes out his own bracelet and a similar combination mechanism shows. Phantom lines it up and doors open up ahead. Everyone follows after him and soon they reach a large hollow chasm of a room with openings for the many canals. A platform in the middle has an altar with crystals embedded in it, with water flowing up towards the top. Phantom begins exclaiming that he was after the crystals, but soon Manaphy decides to swim in the flow of water. But this doesn't stop Phantom, as he pulls out a crystal. Suddenly the water stops and Manaphy falls to May. The temple begins rumbling in an ominous manner. Water begins spurting out of the openings, and it's soon realized that Samiya has become unstable. At this rate, there's no time to stop Phantom, the gang heads back for the submarine. Along the way they meet up with Jackie, who tells everyone to just go back, he'll take care of Phantom.
Everyone heads back for the sub, while back in the treasure room, Phantom is plucking out more crystals. By now the water level in the room has reached about a quarter way, though the altar is safe for now from flooding. Jackie comes in, stopping Phantom from plucking out another crystal. Jackie taunts the pirate, using his acrobatic techniques to evade Phantom, while grabbing a crystal and placing it back in its place. Phantom manages to corner Jackie as he tries to place another crystal, but a column of water splash nearby, throwing both off the platform and they soon land into the flooded area. Both are taken into two different canals. Phantom pops up out onto a canal, finding the crystal just ahead of him. He rushes towards it but the crystal slips away into a smaller opening.
Ash and May worry about Jackie, wondering if he's alright. Suddenly Manaphy jumps out of May's arms and lands in the water. It wants to lead the two somewhere, but Lizabeth is worried that they might not make it back. Ash tells Lizabeth to take off, but stay nearby just in case. Manaphy then leads Ash and May up into the temple once more.
Meanwhile, Phantom decides to call it the quits about the crystals and heads back for his sub, which due to the flooding has drifted elsewhere. By the time he reaches it, Jessie, James, and Meowth are there and they plan on taking sub before Phantom can get in. However just before they can close the latch, Phantom gets a good grip on it and pulls it open, sending the three flying off into the waters to be carried away somewhere. Jackie catches up with Phantom before he could get aboard his sub. Not giving up Jackie so easily, he fights him for control of the sub, which ends up Phantom getting pushed off, and Jackie taking off with the sub, but not before Phantom could grab onto a torpedo to use to escape.
Ash and May find themselves in the treasure room, where Manaphy leaps off ahead to pull on a crystal. Ash and May gets that if all the crystals are in place, then Samiya can be saved. So they begin placing the remaining few crystals into the holes, but they are one short. The water has now begun to flood the platform, and deciding to take no more chances, the three decide to flee. But along the way, Pikachu spots a crystal that found its way on a fountain. Ash picks it up while May runs off ahead towards the edge, hoping to see Lizabeth's sub somewhere. But the flooding is showing no signs of stopping. Luckily the pod that the Rockets took happened to be near by. Ash opens it up and puts May, Manaphy and Pikachu inside. He says he'll put the last crystal in and save Samiya. Despite protests from May, Ash closes the door and runs off.
Jackie reaches the surface to where the Blue Lagoon lies. He asks if Lizabeth and the others have surfaced yet, but Ship says they're still down there since Ash and May went back inside. Jackie's a bit shocked at that, but he stays on the surface since there isn't enough time to save them.
Ash begins his route back to the treasure room by climbing up on the rafters, as the hallway he and May previously took began flooding. He finds the hallway to treasure room, but it's flooded. Taking a deep breath, he dives in and swims into the treasure room. Ash is forced to swim under his own energy and by the time he gets there, he runs out of breath, making him drop the crystal as he frantically scrambles to reach the top of the treasure room, which by now is almost flooded. He catches sight of where the crystal lands, and finds it embedded in a crack at the bottom. He swims down, taking a hold of the crystal but has trouble pulling it out. When he finally gets the crystal, he swims back up but once more his breath runs out and loses consciousness, dropping the crystal.
May begins to worry about Ash, and she hopes for his safety and wishes him luck. Manaphy uses Heart Swap to relay this to Ash, who suddenly gets a burst of energy, enough to get him back to the top of the room once more. Locating the crystal once more at the bottom, he dives down to retrieve, and ignoring how much air he has left, he swims around the altar, setting the last crystal inside. Suddenly a yellow glow fills the room. Samiya in its collapsing state, was about to collide into an ocean cliff, with the crystals in place, the temple barely misses and begins floating upwards. Meanwhile, yellow energy beams begin to snake out from the treasure room, and wrap around Samiya as it floats upwards. At the surface, everyone is back on the Blue Lagoon, and soon sees Samiya rise as the sun is rising as well.
When the temple finally settles on the surface of the ocean, May opens up the pod door. Ash has saved Samiya, but May is afraid that he drowned in the process. But something comes from the ocean behind May. Phantom pops up from the surface from his torpedo, grabbing Manaphy and soon makes a getaway. Phantom has an easy time at first, but then a yellow energy beam shoots out from the water and begins following Phantom. There's someone inside the energy beam though, and sees Ash. He pursues Phantom while the water Pokémon in the ocean begin gathering. As Phantom dives down beneath in hopes to avoid Ash, he's blocked by a school of Remoraid. Taking advantage of the pirate's surprise, Ash takes Manaphy away. He swims away, surprised at how many Pokémon have gathered; even the legendary Kyogre has appeared.
But not all is well; Phantom makes one last effort in capturing Manaphy by staging an attack with his large submarine. Manaphy however hops off from Ash's arms to take control. Manaphy summons all the nearby water Pokémon in the vicinity to launch a counterattack against Phantom's submarine. Most of them gather to hinder its movements while Chinchou slip into an exposed circuitry. They short out the submarine, leaving it a sitting duck. Taking this chance, Manaphy hops onto Kyogre, and Kyogre jumps out of the water, only to launch a Hyper Beam attack on the submarine, critically damaging it and all useful equipment. After the battle, Jackie, using Phantom's personal sub, finds his way to Phantom, where he's seeing him in tattered clothing holding up a heavy piece of a collapsed pillar. Behind the clothing reveals a mechanized suit, in which Jackie figures out how the old pirate was able to have superhuman strength like lifting a boulder up. Phantom's suit though overloads and the column collapses on him. Jackie climbs up on top of the wrecked sub, contacting the Ranger's Base that his mission is complete.
The crew aboard Blue Lagoon are excited to see Ash, especially having been granted the power the King had. To celebrate, Ash takes the others along in their own energy beams to explore the underwater depths around Samiya, to see all the water Pokémon that have gathered around to see the Prince of the Sea. At the end of the day, Samiya sinks down into the ocean once more to be hidden from the world. On the Blue Lagoon, May is with Manaphy, about to release it back into the ocean, this time for good. Though she has a hard time, she manages to say goodbye. Manaphy actually speaks out May's name, expressing how it loves May before jumping off into the ocean. Manaphy then swims towards Samiya.