I don't own Pokemon or the idea of this story which I got from Captain Buggles. I just own my OCs.
TMs will exist in this universe but instead of replacing older moves I will just add to the list like TM02 is still Razor Wind but Headbutt is TM57. I will put a list of TMs in this universe on my profile and I'll just make the HMs TMs as well and I forgot to mention this earlier Ash can carry nine Pokemon on him.
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. Ashley 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 Crawdaunt. 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, Crawdaunt 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. Crawdaunt 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.
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 Butch and Cassidy 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.
Ashley 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. Ashley tells Lizabeth to take off, but stay nearby just in case. Manaphy then leads Ashley 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. 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.
Ashley and May find themselves in the treasure room, where Manaphy leaps off ahead to pull on a crystal. Ashley 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. Ashley 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. Ashley 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, Ashleyz11 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 Ashley 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.
Ashley begins her route back to the treasure room by climbing up on the rafters, as the hallway she and May previously took began flooding. She finds the hallway to treasure room, but it's flooded. Taking a deep breath, she dives in and swims into the treasure room. Ashley is forced to swim under her own energy and by the time she gets there, she runs out of breath, making him drop the crystal as she frantically scrambles to reach the top of the treasure room, which by now is almost flooded. She catches sight of where the crystal lands, and finds it embedded in a crack at the bottom. She swims down, taking a hold of the crystal but has trouble pulling it out. When she 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 Ashley, and she hopes for her safety and wishes her luck. Manaphy uses Heart Swap to relay this to Ashley, 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, she dives down to retrieve, and ignoring how much air she has left, she 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. Ashley has saved Samiya, but May is afraid that she 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 Ashley. She pursues Phantom while the water Pokémon in the ocean begin gathering. As Phantom dives down beneath in hopes to avoid Ashley, 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 Ashley'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 Ashley, 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 type 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.
The Blue Lagoon reaches the port town, with Gabu, Dabu, and Zabu greeting them excitedly at the dock. Ash and company part ways with the circus crew as they head off to their next destination. Jackie, with the help of Officer Jenny finds and arrest Captain Phantom and his crew from the Phantom Troop. In a later adventure, a Zapdos is seen flying through a mountainous region, and is captured by Jackie so he can hitch a ride on it. Various Water Pokémon, including Manaphy, are shown wandering and swimming around Samiya. At the end, Ashley and the gang are seen at camp during the night, conversing around a fire, and after they are shown walking a path in the woods.