Ash and his friends dash through Ogi City to make it to their next ferry, but it's too late and the vessel has already left port. Misty asks a local sailor when the next ferry will come, and he reveals the ferry to Red Rock Isle only comes once a day. Luka walks over to the group, and notices them sulking. Brock is instantly cheered up, but Misty drags him away by the ear before he scares Luka off. Luka offers to give the group a lift to Red Rock Isle in her boat, much to Ash's surprise. Brock is overwhelmingly grateful and grabs a hold of Luka's hands. Team Rocket spies from their Magikarp submarine, and they watch as Luka escorts the group onto her boat.
They soon leave port. On the deck, Ash and his friends inspect Luka's dive gear. Ash notices several pictures near the ship’s wheel and asks Luka about them. A picture of a map with a noticeable X on captivates the group's attention, and to their surprise it is a treasure map. Luka clarifies she came across the map in a journal while looking through her great-grandfather old stuff. The journal spoke of the legendary Silver Wing, a treasure said to have a link to a mysterious Pokémon. Ash recounts the group’s past encounter with their own mysterious Pokémon, but the vague details offer Luka little to go on. Luka continues her story and reveals that her great-grandfather's ship, the I.S.S Raspberry, was caught in a horrible storm and the Silver Wing went down with it. She hopes to finally prove her great-grandfather's story and has since run through some calculations to determine where the shipwreck may be lying. The potential of future instantly excites the boys. Luka likes their enthusiasm and allows them to join her. Team Rocket overhears the news and are instantly intrigued. James is keen to dive down and retrieve it, but Jessie shakes her head. Meowth is on the same wavelength as Jessie, so the trio agree to wait for the group to recover the sunken treasure for them. Jessie adds that they will steal the treasure and Pikachu as well.
Luka soon arrives at the location. She calls out her three Magikarp to act as guides while she and Ash go underwater. Pikachu tries to do the same, but Brock grabs him before he can jump in. Ash assures Pikachu that he’ll be fine. Soon he and Luka grab a hold of a Magikarp each and dive down to the depths. Brock and Misty remain in contact with the pair through the ship’s radio. Underwater seemed to be another world and is teeming with Water Pokémon. Ash soon spots a shipwreck and Luka confirms that it is the I.S.S Raspberry. Luka sends her Magikarp ahead to scout the ship. All of a sudden a Mantine approaches the Magikarp and scares them off. Luka decides that Mantine is too big of a hurdle so she and Ash resurface to plan their next move. They consider using the Magikarp as a distraction, but Ash suggests Pikachu's Electric attacks should work on Mantine. With that, Pikachu joins the dive expedition. In the ocean depths, Pikachu and Ash swim ahead to distract Mantine while Luka ventures inside the wreck. The ploy seems to be working, and Pikachu manages to jump onto Mantine's back. Just as he is about to deliver an electric attack, a Remoraid knock Pikachu off with a Water Gun attack. Luka is also sent backwards by another Remoraid. She swims over to Ash and urges him to retreat, and the pair soon resurface for another break. Team Rocket watched everything unfold from the submarine. Jessie decides they should switch plans and set their sights on the powerful Mantine instead, and her teammates agree.
The group now know they have two obstacles to tackle, Mantine and Remoraid. Misty suggests her Water Pokémon will be useful, so she and Ash call out Totodile, Staryu, and Corsola. Psyduck also appears, but it splashes around frantically because it cannot swim. Brock quickly pulls it back onto the ship with a lifesaver ring. Ash, Misty, Pikachu, and Luka soon go into the water, again for the shipwreck. As they dive down, there seems to be a fight already unfolding between Team Rocket and the Mantine. Luckily the unexpected distraction allows Luka and her diving party to enter the I.S.S Raspberry's hull without any trouble. Armed with a torch, Luka soon spots an odd hole in the wooden interior. Inside, they find a room full of swarming young Remoraid. Luka understands that The Remoraid only attacked because they were protecting their young, but she can’t understand Mantine's connection exactly. Suddenly Team Rocket smash their submarine directly into the ship which causes all of the Remoraid to scatter, and also reveals a small chest. Luka picks up the chest and they decide to return to her boat.
Their departure, however, is interrupted by Team Rocket. The Magikarp submarine's eyes beam a protection onto one of the ship's walls, and the movie featured is Team Rocket's own motto. Team Rocket swipes the chest and they reverse out of the ship. Mantine crashes into the sub, but Team Rocket end up catching it with a sticky thread. It struggles to free itself, though its Remoraid friends use Water Gun to free Mantine. Luka is impressed by Mantine and the Remoraid's friendship and suggests it might be a case of symbiosis. Team Rocket net the wild Pokémon, but Totodile and Misty's Pokémon make quick work of the net. Jessie is annoyed, but she listens to her teammates and so they begin to retreat with at least the treasure chest in their possession. Team Rocket's pedaling puts some distance between them and Ash's group. Though Mantine lets Ash and Pikachu on to its back, allowing Pikachu to deliver a close range attack. The electric surge sends Team Rocket blasting off.
The treasure chest is also sent hurtling into the air. As the precious item makes its descent, Mantine majestically leaps out of the water, with Ash and Pikachu still on its back, as if it were flying. Ash successfully catches the chest. Luka thanks the Mantine and Remoraid for their help before the Water Pokémon swim off. She opens up the chest to reveal a smaller box inside. She opens the box and finds a gleaming Silver Wing resting in it. She holds it in the light and everyone marvels at its radiance for a while. Luka declares that artifact will help her with her research and towards solving the mystery of the mysterious Pokemon. The next day, Luka sails towards Red Rock Isle, where the Ash and Misty look forward to competing in the fast-approaching Whirl Cup Tournament.