With the child Lugia now captured by Team Rocket, it could only stir up trouble with the parent Lugia. Dr. Number stands proud in front of the new catch when Butch and Cassidy show up. They have a plan that they could use the child Lugia to lure the parent so there would be a possibility of having both. The plan would seem almost too easy.
Ash, Misty, Brock, Richie, and Osamu sit depressed upon the shore when Luka comes. She wonders what's going on and they tell her that Team Rocket had captured the child Lugia. Obviously, that's bad, but talkings were cut short when the parent Lugia emerged. Soon every had told about what happened to the child Lugia, which the parent Lugia didn't respond to at first. The parent soon started combing the area but didn't find anything so it went back to the gang. Again they told that the child was captured but they'll do whatever it takes to get the child back. The parent becomes enraged and releases a gigantic storm and wrecking havoc across the island and the neighboring one. With this the gang seek shelter in a cave.
Meanwhile, Jesse still wants to find some way to bring some attention. She still frets about having the chance of taking the child Lugia away gone, but maybe there's something else to it. They hop out of their sub but soon gets blasted by the parent Lugia.
After awhile in the cave, Ash gets an idea, go out there and confront Lugia himself. Stupid, but effective, done it many times. Richie decides he wants to tag along too. Everyone else says it's a way too dangerous to go out in this time, but there's no stopping either. They go out into the ocean by Luka's boat (with her driving it) and eventually catch up. However Lugia fires a beam at them, which Luka dodges easily. This continues for a while until finally it's the either now-or-never situation. A few attempts doesn't make the Lugia phase but soon it calms down and the storm subsides.
With that, now they have a new objective, finding this base. Their Pokemon do a scout of the area but couldn't find anything, but since it's not on land, maybe it's underwater. Ash, Misty, Brock, Richie, and Osamu get in scuba gear and head for the ocean. They couldn't find much, until they notice the Magikarp Sub obviously belonging to Jesse, James and Meowth. They follow that to the base but as soon as they get there, the Rocket's plan soon goes into effect. The base emerges towards the surface!
After the base had emerged, they release the child Lugia still in the cage and with some contraption out there for the parent to get. The gang obviously knows this is a trap and soon the parent Lugia comes by. Everyone soon sees this, the gang yelling not to get any near while running. Then they are stopped by Butch and Cassidy. Since they can't go any further, it would just be easier to attack the parent Lugia from here on to see if it would get the idea. Both Ash's and Richie's Pikachu's go up for an attack, but the parent easily dodges it. Butch messes with a little gizmo and some headgear on their Pokemon glows orange for a while, making them aggresive. They explain that this new device not only keeps them angry, but boosts their abilities. Houndour does a Flamethrower which was significantly more powerful than before. This doesn't stop them however, the gang presists on attacking the parent but everytime Butch and Cassidy have their Pokemon retaliate.
Later, Jesse comes up with another one their schemes, place a fake Lugia in and see if that'll work. Apparently that's taking a bit too long as James and Meowth inflate a Lugia balloon... a little too large.
Butch increases the intensity of the headgear and soon their Pokemon become worse. Ash sends out Cyndaquil and Richie sends out Charmeleon. But all they took was one hit and no more. The gang tries to give the parent again but this time the parent Lugia decided to give them a shot with its attack, though missing, knocks all of them out. The Lugia continues on and the trap activates. The little balloon thing is done, but looks like it's too late, so Jesse, James and Meowth pick it up, but Meowth's claws makes a hole, which blows them away, again. The Rocket's soon retrieve their second catch, going back underwater. Later, Ash wakes up, in the lab, and in a cage.

Thanks to Xeno Lugia for writing This for us