Our heroes take an excursion to the Muraille Coast before Ash's Cyllage City Gym battle. They spend some time fishing until Ash pulls up a Skrelp, which attacks Pikachu with its poison! Fortunately, they meet a couple along the beach road who heal Pikachu with a handy Antidote. Eddy and Lindsey are underwater archeologists in search of the Cussler, a luxury liner that sank many years ago. Our heroes decide to help them with their quest!
While Clemont and Bonnie stay above with Eddy, Ash and Serena join Lindsey in her submarine, and they dive toward the ocean floor. Sure enough, the wreck of the Cussler is there, and thanks to some crafty Dragalge who have fused it together with Acid, it's become a home for many different kinds of Water-type Pokémon!
A mysterious light lures them deeper into the wreckage, where they spot Team Rocket's submarine. The villains have come to claim the Cussler's sunken treasure, and their meddling has endangered the structure of the ship. With a little help from our heroes, the wild Pokémon manage to fix up their underwater refuge. But at the same time, Team Rocket escapes with the Cussler's safe—only to get caught in a whirlpool! Skrelp is caught too, but Froakie comes to the rescue, showing off its spectacular jumping skills…and giving Ash some ideas he would put to use in his upcoming Gym battle against Grant!
Finishing up lunch by the Muraille Coast, Ash is keen to get back to training for his upcoming Cyllage Gym battle. However, Serena decides that they should do some fishing with the rods they received at Ambrette Aquarium since they're at the beach and doing too much training will stress Ash out. Clemont suggests that Ash should catch another Water-type Pokémon, which will make it easier when it comes to battling Grant, to which Ash agrees, so everyone begins fishing. Ash soon gets a bite, but it proves to be quite strong, before eventually bringing up to the surface. Ash is confused by his catch, which Serena tells him it looks like he only caught some kelp. Clemont corrects her, saying that Ash did in fact catch something. However, when Ash examines it closely, the mystery Pokémon goes straight for his face. As Ash pulls the Pokémon away from his face, Bonnie notices that it is hurt and places a bandage on its head. As everyone stares at the Pokémon, it begins to flail about once more before slipping from Ash's grip and back into the water. Ash scans the Pokémon with his Pokédex and learns that it is a Skrelp. Skrelp then fires a Sludge Bomb to defend itself from the group. Pikachu bravely attempts to talk to Skrelp, but is hit with Toxic and becomes badly poisoned in the process. As Skrelp swims off, Clemont tells them they need to get Pikachu to a Pokémon Center quickly, but as they rush off, a van pulls up at the side of the road and a couple offers them help in tending to Pikachu by using an Antidote.
Having used the Antidote, Pikachu is successfully cured from the poison's effects, and Ash thanks the couple for their help. The couple then introduce themselves as Eddy and Lindsey, and reveal that they're underwater archaeologists interested in searching for the S.S. Cussler, a luxury liner that sank due to hitting an iceberg many years ago. They reveal that the Cussler may sit off the Muraille Coast because of strong underwater currents. Becoming interested, Ash and his friends offer to help them in any way they can, to which they accept, admitting that they're shorthanded at the moment. Lindsey mentions that the quest could get dangerous, so the group will need to listen to them and they agree as everyone sets off. However, once they drive off, Team Rocket also heard everything about the Cussler and set their sights on retrieving the treasures inside the shipwreck for themselves.
On the boat, Eddy informs Lindsey that it is almost time, and she tells Ash and his friends to watch the whirlpools very carefully. Upon watching them, the group notices that the whirlpools have now disappeared. This is because the intersecting currents that create the whirlpools regularly change, so the whirlpools aren't around for long. Eddy continues to sail ahead, and soon they arrive at their dive spot. Lindsey prepares to enter the submarine, and has to break the news to the group, that there is only room for two other people to join her. Clemont has a solution to the issue as he reveals his newest invention, a machine that will decide fair and square who wins a chance to go inside the submarine with Lindsey. The machine reveals the winners to be Ash and Serena, leaving Bonnie annoyed with Clemont for them losing the opportunity, but Clemont tells her that their fate was chosen by science, so there aren't any hard feelings.
With the winning group now decided, it is time for them to dive down to the depths in search of the S.S. Cussler. Lindsey radios through to the bridge, and Eddy confirms that their audio visual communication system is working well. Down in the submarine, Serena watches a group of Qwilfish swim by, while Ash mentions the amount of Octillery on his side. Serena is impressed by the amount of Water-type Pokémon there are as the submarine continues to go deeper into the ocean. Serena notices three Skrelp, and recognizes the one they encountered earlier by the bandage Bonnie put on its head. As Serena and Ash are happy that Skrelp managed to find its friends, the submarine is suddenly caught up in the current, which causes an interference with the communication system. However, Lindsey isn't fazed by it but is instead excited that their theory about how the Cussler got swept away is proving to be correct. Serena becomes worried as the ship is quite close to them, but Lindsey handles things and gets them to safety. Ash notices the group of Skrelp following the sunken ship and Lindsey decides to follow them. They notice a distinctive Milotic emblem on the ship's hull, which Eddy confirms is the Cussler. Two Pokémon emerge from the Cussler and approach the sunken ship from earlier as Ash scans the unfamiliar Pokémon with his Pokédex, learning that the two Pokémon are Dragalge. Lindsey then states that the Dragalge appear to fusing the two ships together as a group of Luvdisc, Chinchou, and Remoraid emerge from the Cussler and begin playing with the group of Skrelp. Eddy explains that the Dragalge used Acid to fuse the two ships together to create one whole structure for a bigger home. After watching how well the Water-type Pokémon get along, Lindsey then notices a bright light coming from the side of the ship, as do the Water Pokémon.
The Dragalge approach the light to investigate further, but it turns out to be Team Rocket's Magikarp submarine cutting through the side of the shipwreck. Lindsey follows in the submarine, upon arriving, Ash immediately recognizes the submarine as Team Rocket's. The sudden mention of the name confuses Eddy, though Clemont explains that Team Rocket steal Pokémon. Team Rocket enter the Cussler’s hull and locate an air gap to begin searching for treasure. Soon, the Skrelp and Dragalge emerge from the water, followed by Lindsey's submarine. Ash opens the lid of the submarine, but there is no sign of Team Rocket. Serena also looks outside, but the Skrelp and Dragalge notice and begin to fire Acid at them, until Pikachu steps in and is recognized by the Skrelp with the bandage, who tells its friends to stop attacking. Skrelp then goes after Team Rocket as they are busy setting up to steal the safe. An Acid attack is sent towards James's feet as the Skrelp with the bandage shows itself to them, telling them to leave or they're going to pay. Jessie corrects it, announcing that they're going to get paid after they obtain the treasure. Ash and the others demand to know what Team Rocket are up to. Jessie presses a button on a remote, revealing that the safe will blast off in mere moments. As smoke fills the entire area, Team Rocket use this as cover to make their escape. As Team Rocket run, Skrelp takes off after them, and Ash sends out Froakie to follow Skrelp. Lindsey warns everyone that they need to get out immediately because once the safe opens up a hole, the ship will fill up with water.
The safe breaks through the hull walls of the ship, creating a hole and heading straight for Team Rocket's submarine. However, as Team Rocket prepare to grab the safe, Skrelp floats in front of the periscope, startling Jessie as the Skrelp attacks their submarine with Sludge Bomb. Froakie then looks into the periscope as Jessie tries to shake him off, but he holds on tight. Lindsey's submarine emerges from the Cussler, and Lindsey fears the shipwreck will collapse from taking on too much water. Ash is determined not to let this happen, so he recruits the Dragalge and the other Water Pokémon to help out. The Pokémon try to hold the Cussler up, but change strategy after Ash suggests they seal it shut with a metal plate. The Dragalge use Acid to attach the metal seal to the Cussler, which does the trick as the structure stops collapsing.
Eddy radios in, glad to hear that the Cussler is safe, but warns Lindsey that the whirlpools are scheduled to return again. Now with the Cussler’s safe in hand, Team Rocket return to the surface, but find themselves surrounded and trapped by swirling whirlpools. The Magikarp submarine is eventually pulled into the vortex, blasting Team Rocket off and separating them from their stolen safe. As Lindsey, Ash, and Serena come to the surface in their own submarine, Ash wonders where Skrelp and Froakie are, eventually noticing that they're both trapped in a whirlpool. Lindsey reveals that not even Water-types are able to withstand the whirlpools. Ash desperately tells Froakie to jump. Froakie orders Skrelp to get on its back before making several jumps across several bits of debris. After successfully jumping, Froakie finishes off with one last big jump and is safely caught by Ash, and everyone is relieved that they are both alright.
As the evening set in, Ash and his friends wave goodbye to the Skrelp and Dragalge, who return to their underwater home. Eddy reveals that they were able to pinpoint the exact current that carried the Cussler to the location it is now, but Lindsey remarks that she was impressed by the many Pokémon living down there, and that they were the real discovery. As Clemont compliments on Froakie’s incredible leap, Ash suddenly realizes that such a big leap might help him defeat the Cyllage Gym.