Dr. Namba, Butch and Cassidy gaze at their captured parent Lugia, and so they whisk the child off to another room. Ash and Ritchie are determined to fulfill their promise to Lugia, but with their Poké Balls separated from them the situation looks dire. The lights suddenly come on and Dr. Namba greets his captives. He declares that Pokémon are designed to serve humanity, but Ash and the others refute these claims. Dr. Namba brags about his headband devices used by Butch and Cassidy earlier, the “Namba’s Nasty Pokémon Provoker”, which harnesses the power of rage to make a Pokémon more powerful. He plans to do the same to Lugia, but he decides to demonstrate the technology on Sparky and Pikachu first.
Later, Oliver leaves Luka and the safety of the boat to rescue Ash and the others. He and Lanturn locate Team Rocket's underwater base and Oliver slips inside through an opening. Meanwhile the Team Rocket trio gain access into the security room, and are pleasantly surprised to that Ash and his friends have been captured. Jessie orders her teammates about. Soon Oliver emerges from the ventilation system, but he is immediately spring by a Team Rocket Grunt. Jessie and James notice the scene and spot an opportunity. They take over, but Oliver continues to struggle to free himself. Jessie whispers into Oliver's ear, and they enlist his help with their own scheme. Oliver asks who are they, and Jessie and James simply refer to themselves as "superheroes".
Dr. Namba's test on Pikachu and Sparky begins. The group distracts Namba with their pleas. Oliver breaks in through a ventilation shaft and punches in the lock code, opening the door from the cage. Ash tackles Dr. Namba into a wall and then breaks the mechanism before the power headbands can be placed on the Pikachu, and smashes the claw directly into the control console. Brock and Misty also gather everyone’s Poké Balls. Ash and the others thank Oliver, and he reveals that he received help from some "superheroes". Dr. Namba presses an alert button, and as the group tries to leave the facility they find themselves surrounded by Team Rocket Grunts. Butch and Cassidy call on their Pokémon with the power headbands on them. Houndour starts off with a Flamethrower and Hitmontop uses Rolling Kick, but Pikachu and Sparky easily dodge both attacks. Ash and Ritchie have a plan though, they have their Pokémon aim their Thunderbolts at the gadgets. The Thunderbolts destroy the headbands as planned. With the Pokémon powerless, both Pikachu do a head on Tackle and knock them out. The battle is cut short when Dr. Namba alerts his Butch and Cassidy to some activity in Lugia’s area. Totodile and Cruise make quick work of the remaining Rocket Grunts.
Butch and Cassidy arrive and are disturbed to see their rivals, Jessie and James, working to free the Lugia. The two Rocket teams get into a heated battle. Jessie and James send out Arbok and Victreebel respectively. Cassidy's Houndour misses one Flamethrower, hitting a support for the energy barrier that is keeping Lugia trapped. Butch's Hitmontop tries a Rapid Spin, but is disrupted by Victreebel's Vine Whip, hitting the support again. Another break occurs when Arbok is slammed into the support. Jessie calls on her Wobbuffet and he Counters another of Houndour's Flamethrower attacks. The result is cataclysmic and the parent Lugia is subsequently freed. With that, the parent Lugia goes berserk on the base, firing a beam at random locations. One blast hits the Rockets, blowing them all into the sky. The beam also causes a breach of the base's protective walls, which causes the base to rise to the surface.
Ash and his friends soon reach Silver, but Dr. Namba is standing in their way. He sends out an Electabuzz with the provoker headband device. Ash and Ritchie send out their Pikachu to do the job. Electabuzz goes for a Thunder Punch, leaving a crater in the floor, but the Pikachu manage to dodge the attack. They retaliate with a Thunderbolt but Electabuzz uses Light Screen and the bolts simply bounce off. Electabuzz unleashes a more powerful Thunderbolt, hitting both Pikachu easily. Namba continues to dial up the rage level of his Electabuzz, making Pikachu and Sparky's attempts useless. Ritchie suggests they aim for the controller in Dr. Namba's hands, and Ash agrees to the idea. Pikachu acts a distraction, and while Dr. Namba focuses on the battle, Sparky delivers a direct shock and breaks the controller. The Electabuzz snaps out of its rage, and the two Pikachu perform a double Thunder attack to knock it out. Afterwards, the group works on opening the Silver’s cage. Cyndaquil and Zippo use Flamethrower to heat up the metal cage. Poliwhirl and Totodile follow up with a Water Gun attack to cool it down. The sudden changes in temperature causes the metal to become brittle. Cruise bashes its way through the bars to free Silver. Oliver is glad to see his friend again, and the pair exchange a hug.
The parent Lugia continues to Aeroblast its way through Team Rocket's base, causing incredible damage. Ash and his friends wheel Silver through the hallways and stop when they spot its parent. Ash attempts to reason with Lugia, but it is too berserk to listen. Silver calls out to its parent, and this instantly calms Lugia down. Misty looks above her and notices debris is about to hit everyone. They shield themselves in anticipation, but Lugia protects them from harm with its Safeguard. The group realizes Lugia now trusts them and they thank it. Soon they start to make their way out of the base and dive for the ocean. The base finally explodes, but the mighty ocean drags the debris down to the seafloor. Namba and several grunts are later seen floating on some debris.
By evening, everyone is back on Luka's boat. The two Lugia prepare to leave and soon swim out into the ocean depths. Oliver tears up as he watches his friend leave. Misty offers Oliver some comfort, and Oliver accepts that Silver may visit again sometime. The Lugia call out to Ash and the others and receive a wave goodbye in return. The next day, Ritchie decides to explore the Whirl Islands further and promises to battle Ash the next time they meet. Oliver remains on Ogi Isle as well, while Luka escorts Ash and his friends to Transit Town.