With the young Lugia in the possession of Butch and Cassidy, Ash and friends set about rescuing it while protecting its parent from itself. The parent Lugia fights desperately to free its child—playing right into Team Rocket's hands. If Ash fails to win the Lugia's trust and convince it not to oppose Team Rocket alone, it seems this Pokemon is fated to end up in captivity along with its child.
With the childLugia now captured by Team Rocket, Dr. Namba proudly stands in front of the new catch as it cries. Butch and Cassidy show up and suggest they use the child Lugia as a lure to capture its parent. Dr. Namba cackles as the plan seems almost too easy.
Luka returns to her friends by nightfall with supplies in her arms. She notices everyone is looking sad and they inform her that Team Rocket has captured Silver. Luka is shocked, but they have little time to discuss a plan. The parent Lugia suddenly emerges from the sea as it frantically searches for its child. Oliver tries to calm Lugia down, but he is too upset by the situation and begins tearing up. The parent becomes enraged and releases a gigantic storm that wreaks havoc across the island and the neighboring one. The dreadful conditions forces everyone to seek shelter in a cave. The large waves crash Team Rocket's Magikarp submarine into a seawall, forcing the trio to abandon their vessel. The parent Lugia soon flies overhead and in a rage it Aeroblasts them off. Meanwhile, Dr. Namba watches the scene from the safety of his underwater base. One of the Team Rocket Grunts alerts him to the increasing surge in power, but Dr. Namba sniggers.
Luka's Silver Wing continues to beam a frightening red light as Lugia continues its destruction. After a while in the cave, Ash decides that he is going to face Lugia and try to get it to believe them. Ritchie agrees, and goes with Ash. Luka offers to drive her boat and together the three head towards Lugia. However Lugia fires a beam at them, which Luka dodges easily. This continues for a while until finally it's a now-or-never situation. Eventually, Lugia calms down and believes Ash and Ritchie when they promise to find its child. Lugia stops the storm and flies away.
With that, now they have a new objective, finding Team Rocket's base. Their Pokémon do a scout of the area but cannot find anything. Ritchie notices that Silver hadn't responded whatsoever, and considers that Team Rocket are likely still in the area hoping to catch the parent as well. Everyone decides an underwater search is in order. Misty calls on her ensemble of Water-types and Ash sends out his Totodile. Soon enough, Oliver's Lanturn seems to have found something, so everyone puts on their scuba gear and dives into the ocean. They don't find much, until they notice Team Rocket's Magikarp Submarine and they follow it directly to Dr. Namba's operational base.
Dr. Namba authorizes the next plan, and so the underwater base ascends to the surface. The Rocket trio, who snuck on board, find themselves sealed off and their small compartment fills with water as the entire base lifts from the seafloor. Luka spots the base surface in the horizon and is instantly alarmed by the potential threat. After the base had emerged, they place the child Lugia still in its cage and with some contraption onto the shore and wait for its parent to arrive. Luka pulls the dive party aboard and steers them to the coast. Ash, his friends and Ritchie get off once Luka docks the vessel. Oliver is keen to go as well, but Luka demands he wait with her. Ash and the others notice the parent zeroing in on its child and they try to warn it, though Butch and Cassidy stand in their way. The Rocket duo send out Houndour and Hitmontop, and Cassidy activates a special headband that powers up the two Pokémon. Ash and Ritchie send their two Pikachu to use Thunderbolt to stop Lugia from falling for Team Rocket's trap. But Cassidy has Houndour aims a Flamethrower at the pair. Ash and Ritchie send out their own Fire power, Cyndaquil and Zippo respectively. The group try to keep Lugia at bay, but Cassidy and Butch counter each of their attempts. Hitmontop knocks Cyndaquil and later Misty's Poliwhirl out with its enraged Triple Kick, while Zippo is recalled after being hit by a powerful Flamethrower. The group tries to warn the parent again, but this time Lugia lashes out at them with an Aeroblast. Lugia reaches its child and the trap activates, holding Lugia captive in a field of energy. Meanwhile, the Team Rocket trio is ready to put their surrogate Lugia balloon plan into action. However, Meowth accidentally pops it with his claws and it sends the trio blasting off.
Luka and Oliver watch helplessly from the boat as both child, and now parent are held captive by Team Rocket. The base soon returns to underwater. Ash wakes up later, only to find himself, Misty, Brock and Ritchie in a cage.