The story left off with Ash and the gang, along with Richie, captured by Team Rocket and held at their base. Dr. Number 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 gang wakes up and figures out what to do, Ash rambling about the whole incident. Soon Dr. Number 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 Pokemon were part of his little expirement 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, Osamu decides that he wants to go rescue them and tells Luka that he's going down there and get them back. Jesse, James, and Meowth are later looking in a security room for any hints on where the parent Lugia might be at. Osamu enters the base and ends up in the vents, then finds his way into a hall, but a Rocket has caught him. Jesse and James are there and know that Osamu could be helpful, so they fake the Rocket and take over, telling Osamu where the gang is.
Dr. Number shows the gang how this little mechanism works, the test subjects are Ash and Richie's Pikachus. They come out on a elevator-table restrained while a hook lowers the mechanism down. But just before that could happen, Osamu breaks in and punches in the lock code, opening the door from the cage. Ash slams in the Dr. Number and then breaks off the hook thing and uses that to break the console. (whoa...) They try to get everything back together again, thanking Osamu while their at it. Dr. Number however, trips the alarm and the whole base comes towards the room. The gang tries to run out but are cut off by Butch, Cassidy, and a whole mess of Rockets. Butch and Cassidy release their Pokemon with the same gadget on them. They start off with a Flamethrower and Rolling Kick but Ash and Richie's Pikachus dodges both easily. Ash and Richie have a plan though, they have their Pikachus use Thunderbolt, but aim for the gadget, which breaks it. With the Pokemon 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 Jesse and James' favor as Arbok and Weepinbel 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 Weepinbel's Vine Whip, hitting the support again. A final break happened when Arbok got slammed into the support, the parent Lugia soon free. With that, the parent Lugia goes beserk on the base, firing a beam at random locations, perferebly towards the Rockets, blowing them into the sky. The beam cuases a breach, which causes the base to rise to the surface.
With the other Rockets to take care of, Ash sends out Totodile and Richie sends out Pupitar. Totodile shoots a Watergun towards them and Pupitar hits them hard with a Tackle, getting them all. They find the room where the child Lugia is at, but it's guard by Dr. Number. He sends out a Electabuzz with the head mechanism. Ash and Richie send out their Pikachus to do the job. Electabuzz goes up for a Thunder Punch, litterally making a crater, but the Pikachus manage to dodge. 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 Pikachus 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 Richie 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. Number 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. Number 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, then Totodile to do Water Gun which rusts it, then Richie has his Pupitar 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 and decides to trust them. Soon they start to make their way out of the base and dive for the ocean.
In the evening, the two Lugias go head back for the ocean, probably never returning but who knows? The next day, Richie decides to stay on the island with Osamu for a while, Ash and the others have a League to finish off. They say their goodbyes and go their seperate ways.

Thanks to Xeno Lugia for writing This for us