The story leaves off with Ash and his friends, along with Ritchie, captured by Team Rocket and held at their base. Dr. Namba and the other Rockets look upon their capture of the parent Lugia, but they rather use that than the child so they carry that one off. Later, the group wakes up in a cage separated from their Poké Balls and try to figure out what to do. Soon Dr. Namba comes in and tells them his plan, after all they won't be long before they put it into effect. The head item that was on Butch and Cassidy's Pokémon were part of his little experiment of amplifying energy, but also manipulation. If a single Houndour's power is amplified so much to what it was performing at, think how powerful the energy would be from Lugia if amplified.
Later, Oliver decides that he wants to go rescue them and tells Luka that he's going down there and get them back. Jessie, James, and Meowth are later looking in a security room for any hints on where the parent Lugia might be at. Oliver enters the base and ends up in the vents, then finds his way into a hall, but a Team Rocket Grunt has caught him. Jessie and James are there and know that Oliver could be helpful, so they fake the Rocket and take over, telling Oliver where the group is.
Dr. Namba shows the group how this little mechanism works, the test subjects are Pikachu and Sparky. They come out on an elevator-table restrained while a hook lowers the mechanism down. But just before that could happen, Oliver breaks in and punches in the lock code, opening the door from the cage. Ash slams into Dr. Namba and then breaks off the hook thing and uses that to break the console. They try to get everything back together again, thanking Oliver while they're at it. Dr. Namba however, trips the alarm and the whole base comes towards the room. The group tries to run out but is cut off by Butch, Cassidy, and a whole mess of Rockets. Butch and Cassidy release their Pokémon with the same gadget on them. They start off with a Flamethrower and Rolling Kick but Pikachu and Sparky easily dodge both attacks. Ash and Ritchie have a plan though, they have their Pokémon use Thunderbolt, but aim for the gadget, which breaks it. With the Pokémon powerless, both do a head on Tackle and knock them out. They're soon cut short of the battle when they leave off to make sure the parent Lugia doesn't go anywhere.
In the room where the parent Lugia is, James and Meowth do their best to try to free the Lugia. Butch and Cassidy soon run into them, which ends up being a battle between the two. The battle seems to be on Jessie and James's favor as Arbok and Victreebel seem to just easily make comebacks. Cassidy's Houndour misses one Flamethrower, hitting a support for the energy barrier that's keeping Lugia in. Butch's Hitmontop tries a Rolling Kick, but is disrupted by Victreebel's Vine Whip, hitting the support again. A final break happened when Arbok got slammed into the support, the parent Lugia soon freed. With that, the parent Lugia goes berserk on the base, firing a beam at random locations. One blast hits the Rockets, blowing them into the sky. The beam causes a breach, which causes the base to rise to the surface.
With the other Rockets to take care of, Ash sends out Totodile and Ritchie sends out his Pupitar, Cruise. Totodile shoots a Water Gun towards them and Cruise hits them hard with a Tackle, getting them all. They find the room where the child Lugia is at, but it's guarded by Dr. Namba. He sends out an Electabuzz with the head mechanism. Ash and Ritchie send out their Pikachu to do the job. Electabuzz goes up for a Thunder Punch, literally making a crater, 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 does a more powerful version of Thunderbolt, getting both Pikachu easily. Later, the parent Lugia seems to be doing fine causing massive damage. It bursts through a wall to a hallway and then continues to fire beams around.
Ash and Ritchie try to figure out a way to beat Electabuzz. First they tried to outsmart it, but it never seems to work. The Electabuzz catches them in a Thunder Punch combo, but doesn't make contact just yet, giving Ash some time. Then he notices the little controller Dr. Namba has and gets the idea that's what will make the Electabuzz normal. Ash has Pikachu do a Thunderbolt to the Electabuzz, which does a Light Screen. With Electabuzz busy, Sparky goes up to Dr. Namba and shocks him along with the controller, breaking it. The Electabuzz snaps out of it and the two do a double Thunder attack. Afterwards, they work on opening the child Lugia's cage. Ash calls out Cyndaquil to do a Flamethrower, which toasts a part of it. Misty tells Poliwhirl to do Water Gun which rusts it, then Ritchie has Cruise do a Tackle which finally releases the child Lugia.
They carry the child Lugia and run out for an exit, but they stumble into the parent Lugia. Again, they all persuade it to stop attacking and ensures that the child Lugia is safe. The parent Lugia takes a moment but a large piece of debris starts to fall on top of the gang. In a flash, the parent Lugia covers them using Safeguard, and the group realizes that Lugia now trusts them. Soon they start to make their way out of the base and dive for the ocean. Just then, the base explodes. Namba and several grunts are later seen floating on some debris.
In the evening, the two Lugia go head back for the ocean, probably never returning. The next day, Ritchie decides to stay on the island with Oliver for a while, Ash and the others explain they have to head back to Olivine City. They say their goodbyes and go their separate ways.
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