The episode begins with a pair of Wingull circling overhead, and Pikachu and Piplup alone on the beach of a deserted island in the middle of the ocean. The two Pokémon are clearly worried. They call out to their Trainers, but except for large rocks jutting from the water's surface offshore, it's nothing but ocean as far as the eye can see. They look at each other, wondering what to do. A few hours earlier, Ash, Brock and Dawn are on a ship from Iron Island from the previous episode, continuing to Dawns's Contest in Chocovine Town. Ash and Brock are taking in the fresh ocean air near the bow (the front), and the two old friends agree to enjoy it while it lasts. Dawn comes around the corner looking for something, and asks them if they've seen Piplup. They haven't, and it occurs to Ash that he hasn't seen Pikachu either. In an operations section of the ship, Piplup is happily exploring where he shouldn't be, and Pikachu follows, trying to convince him to leave and keep him out of trouble. When Piplup hops on top an exposed, moving gear system and uses it as a treadmill, the alarmed Pikachu shoulder-tackles him off to the other side. Piplup isn't too pleased with this, but the older Pokémon rebukes Piplup, pointing out the danger he had put himself in. Just then, a disguised Team Rocket approaches and Jessie picks up Piplup, proclaiming that she has found her 'long lost Piplup'. While both protest, Meowth asks Pikachu to play along, and when Jessie walks off with Piplup he still protests. James pretends to think that Pikachu wants to come along with them and picks him up too. Ash, Dawn and Brock walk to the stern (back) looking for the Pokémon. Ash wonders where they are, and Dawn states that this always happens: she turns her back on Piplup for only a moment and he disappears. Brock suggests that since he's a curious Pokémon, he's probably exploring the ship. They reach the stern and catch Team Rocket entering their Magikarp Submarine, which is standing on suction cup feet on the deck, with the missing Pokémon in a glass capsule clamped onto the back. They taunt the Trainers, shut the hatch and leap the sub into the ocean. Ash sends out Buizel and before his friends can stop him, Ash leaps from the railing into the water. His Trainer using his collar as a hand hold, Buizel zooms after the sub with Ash in tow. Team Rocket is quite pleased to have captured two Pokémon, and when they see Ash and Buizel gaining on them are determined to out-pedal them. The Magikarp sub is suddenly and violently pulled in another direction by a massive current: they've driven themselves right into a whirlpool. Buizel stops short of the current and can go no further. The Rockets pedal as hard as they can just to stay in control, but as Pikachu and Piplup are bounced around like ping pong balls, the violent shaking suddenly causes the capsule's clamp to open. The capsule is thrown free into the current, and its middle section is smashed open against the rocky bottom. Pikachu and Piplup are quickly swept away in the current and when Ash cries out in alarm he loses his air, forcing Buizel to rush him to the surface. Team Rocket is also swept away in another direction. Beyond two large whirlpools, Ash and Buizel break the surface, when a siren catches their attention. A police boat piloted by an Officer Jenny comes up beside them, and Jenny asks if he's Ash; Brock and Dawn sent out an SOS on his behalf. She pulls them aboard and meets up with the ship to pick up Brock and Dawn. The captain agrees that his ship will continue on to Chocovine Town and once the Trainers have rescued their Pokémon, Jenny will meet up with the ship to escort the Trainers back to him. Jenny's boat speeds off on their way. At the deserted island, Piplup runs out of the water and onto the beach with an unconscious Pikachu on his back. Exhausted, he dumps Pikachu onto the sand and catches his breath. Pikachu wakes up, thanking Piplup when the Penguin Pokémon asks if he's okay. They glance around where they are, seeing only the rocky cliff face behind them, the beach, and the large gray rocks in the water. Piplup's stomach growls loudly, and Pikachu tells him to wait on the beach while he looks for food. Quickly scaling the cliff face, at the top Pikachu finds a grassy meadow with some Nosepass and Probopass, some Wingull flying by a forest on the other side of the meadow, and further along, a small mountain looming above the forest. Pikachu gets excited at this; there must be food sources around to support these Pokémon. He runs into the forest and looking around, easily finds an apple tree. Leaping up into the branches, he picks several to fall to the ground then jumps down to retrieve them. A mysterious twinkle of light catches his eye from the mountain, but it's not clear just what it is. The starving Piplup can only lay on the sand, until Pikachu dumps the apples at his feet and tells him to eat his fill. Piplup gobbles up three right away, as Pikachu looks on and smiles. Now caught up with the start of the episode, Pikachu gets an idea and has Piplup follow him up to the meadow. Dark storm clouds begin gathering over the island as they reach the top. Pikachu explains that if they fire Thunderbolt and BubbleBeam into the sky, the ship may see this and know where they are. It quickly turns into an impromptu competition of who can fire their attack the farthest, as the Wingull fly out to the ocean, away from the growing storm clouds. Pikachu and Piplup don't notice the clouds and Thunderbolt ends up bringing down a lightning strike on them, knocking out Piplup. Pikachu shakes him by the shoulders, but it's the rain that makes him come to. They run into the forest for shelter, right on the heels of the Nosepass and Probopass. With the thunderstorm brewing near the horizon, Officer Jenny and the Trainers kneel over a topographical map of the area from a book. Jenny says the undercurrents would have swept the Pokémon in the general ocean vicinity, but cautions that the area is referred to as Diablo's Ocean. There is a deserted island within the area, and there have been many reports that boats approaching it have had their instruments stop working or even break. She turns the page to a picture of the large gray rocks and cites those as the cause; they surround the island and give off a strange, unknown energy. She adds that a massive survey of the area is being planned very soon. When Dawn asks if the Pokémon could have ended up there, Jenny believes that it's a possibility. That's good enough for Ash, and he sends out Buizel and Staravia to scout the island. Brock thinks that they should follow and Jenny agrees. Pikachu and Piplup are sheltered under a tree beside a small river, when they see a group of Mantyke going upstream with chunks of gray rock on their backs. Curious, Pikachu and Piplup follow them further up the mountain to the bottom of a waterfall, where the Mantyke deliver the rocks to a Corphish beside the waterfall. The Corphish then piles them around a purple, oval crystal. Corphish happily greets the newcomers when the crystal begins to glow with an inner green light. Corphish and the Mantyke become excited as energy comes out of the rocks and is absorbed by the crystal, which then floats up into the air. But then the light fades and it falls back onto the rocks with a musical ring. Pikachu and Piplup give each other a questioning look. The sky has cleared up by the time Corphish leads Pikachu and Piplup to a different spot on the beach, in front of a rocky overhang. It explains that during another thunderstorm, it had taken shelter here when it saw something flying toward the island under the cloud cover, trying to avoid the lightning. It's struck once and falters but keeps flying, as a group of Mantyke also take notice. A closer look reveals it to be a Deoxys, which is then struck down by another lightning bolt. It goes into a crash trajectory and begins to glow green. As it passes over three gray rock pillars, the pillars glow green and fade in turn. Deoxys crashes beside the waterfall, and by the time Corphish and the Mantyke get there, there is nothing but its crystalline organ floating in the air. It lands on the ground and its light fades. Corphish realized that Deoxys and the gray rock are connected, and so along with the Mantyke began breaking the rock apart and placing chunks around the crystalline organ. When the organ glowed the first time, Corphish was proven to be correct. Pikachu and Piplup quickly volunteer their help to get more rock, and Pikachu dives in with the others after taking a gulp of air. They swim down to the lower part of the gray rocks and get to work, the Mantyke using Water Gun to break up the rock. Pikachu, riding on a Mantyke, almost uses Thunderbolt when Piplup reminds him that it would shock everyone else. Piplup then helps out with BubbleBeam. Pikachu takes a look around and spots a boulder-sized rock held up by a thin piece of rock. He climbs up a tall gray rock high above the water, takes in a deep breath and dives, using his momentum to effectively strike with Iron Tail. They head back to the waterfall with their chunks of rock and four Mantyke carrying Pikachu's boulder with him riding on top of it. Staravia and Buizel finally reach the island and spotting the group, immediately head back toward Jenny's boat. When they see Staravia and Buizel, the Trainers know they've spotted something, and Ash urges Officer Jenny to hurry. The Pokémon place the new rocks and Pikachu's boulder beside the crystalline organ and wait. The organ glows again and floats in the air, absorbing the energy. It also extends two tendrils of energy and rub Pikachu and Piplup on the head in thanks, as a pleased Corphish and the happy Mantyke look on. Suddenly, Team Rocket's sub suddenly surfaces from the river, having caught up to Pikachu and Piplup. They extend a mecha arm to capture them when Corphish uses Crabhammer to destroy it. Incensed, the Rockets use a tougher, golden arm to swat away Corphish and complete the capture. Corphish can only look up in frustration as the Rockets celebrate. Staravia comes out of the sky with Quick Attack and breaks the arm, and then Buizel leaps up from the river and uses Water Gun to destroy the hand, freeing Pikachu and Piplup. Staravia and Buizel then join the others on shore. Officer Jenny's police boat comes racing up the river, taking a sharp turn beside the sub as Ash, Brock, and Dawn leap on top of the Magikarp sub and jump down onto shore, relieved that their Pokémon are okay. Jenny proclaims to Team Rocket that they're under arrest, but they scoff at this and recite their motto. Ash yells at them to give it up, and Jessie and James each take out a Poké Ball, ready to battle and steal Pikachu and Piplup. Suddenly, the crystalline organ bursts with light, immediately getting Ash, Brock, and Dawn's attention. The organ floats high into the air, the light recedes a bit, then Deoxys (Normal Forme) fully regenerates to the Pokémon's delight and the humans' amazement. When Dawn asks Ash who that Pokémon is, he easily identifies it as Deoxys. Brock explains that Deoxys is said to come from space, and a Pokémon full of mystery. Team Rocket (of course) decides to switch gears from Pikachu to try capturing Deoxys. The DNA Pokémon then lights up its crystalline organ and levitates the gray rocks, with energy flowing over them. Officer Jenny recognizes the rocks as the ones surrounding the island. Deoxys draws as much energy as it can from the rocks and into its crystalline organ. Jenny notices her instruments suddenly going crazy, only to look up and see that her boat is being dragged toward shore. Team Rocket's sub has levitated out of the water and is floating in the same direction, with the Rockets still on board and scared out of their wits. Brock realizes that the rocks must be meteorites and shouts to Jenny to get her boat out of range, which she does. Brock believes that Deoxys is converting the meteorites energy to its own power, and the side effect is a strong magnetic field. With the sub still floating toward Deoxys, Jessie decides to have Yanmega attack it. Deoxys stops absorbing energy, dropping the meteorites, and changes to Attack Forme to fire Zap Cannon. The attack slams into Yanmega and keeps pushing, slamming her into Pikachu's boulder and sending both into Team Rocket's sub, with the Rockets unable to do anything but panic. The boulder is broken in two pieces on impact, while the attack fries the sub and makes it explode, shattering the boulder and sending Team Rocket blasting off again. The falling remains of the meteorite boulder and the sub threaten everyone below. Deoxys flies over the Mantyke in the river, destroying and deflecting debris with its arms and legs. With them safe, it uses Speed Forme to rush over where the Trainers are, changes into Defense Forme, and dropping over them like a protective dome with the meteorite debris smashing to bits on its back. With the danger over, it flips off and returns to Normal Forme. Ash thanks Deoxys and so do all the Pokémon as Officer Jenny's boat returns to the waterfall. Deoxys looks up at the sky and creates an aurora that everyone enjoys in awe. The DNA Pokémon floats upward as it prepares to leave, and all the Pokémon express their farewells. Deoxys nods in thanks, then flies away to disappear into the aurora. Ash marvels that Pikachu and Piplup had the chance to become friends with Deoxys. As the sun sets, Officer Jenny pilots the police boat across the ocean, and she hypothesizes that the Deoxys go to the island and use the sunken meteorites to reenergize themselves. Brock agrees, as the meteorites come from space, and Deoxys is said to come from space too. Dawn reflects at the fact that there is a Pokémon that uses meteorites to receive its power, and how wonderfully mysterious that is. Ash adds that Deoxys isn't the only one, and that there are many more mysterious Pokémon out in the world that haven't even been discovered yet. Pikachu and Piplup excitedly point out their destination which is now in view, and Jenny confirms that it's Chocovine Town. With Pikachu and Piplup having helped a Pokémon in need, the journey continues.