Ash and his friends are still training on the beach for Ash's upcoming rematch at the Dewford Gym. Brock runs ahead with a whistle, blowing it every so often to make the others keep up. Ash and Max are a few feet behind him, the Pokémon behind them, and May lags behind exhausted. After some time, Brock stops. Ash asks why he stopped and Brock points to a large object on the edge of a cliff some distance away. Everyone stares at it, wondering what it could be. The object turns out to be Professor Birch, who is inspecting a Wingull nest on the cliff. As he does so, the mother Wingull returns and begins to peck at him. He falls down, landing on none other then the sleeping Loudred! He gets up and notices it, but is blown back by a giant rush of sound from the Pokémon. He falls over stunned as the Loudred angrily marches off. Ash and the gang approach and greet him. The group then sits on some rocks and begin to catch up with each other. Ash asks Professor Birch what he is doing in Dewford, and he informs them that it is the Wingull's nesting season, and he likes to study them in their natural environment.
Professor Birch goes on, explaining that he likes to do field work instead of sitting in a lab all day. May doesn't get what's so great about those Wingull nesting, but Max cuts in, arguing that everything about Pokémon is important. The Professor laughs, commenting that Max really likes Pokémon. He then turns to Ash and asks him if he challenged the Gym Leader yet. Ash is embarrassed, saying he kind of lost while laughing nervously. Team Rocket spies on Ash and friends from behind some rocks. They wonder what the Professor is doing all the way out here, then Meowth makes a comment on how he must have some valuable Pokémon with him, enticing the team. Ash and the gang crowd around Professor Birch and explain to him how Ash is battling through the gyms while May just wants to compete in contests. The Professor likes this and asks the group if they would like to join him in his research today. Ash, May, and Max are overjoyed, but Brock isn't too thrilled.
He blows the whistle and holds out a contract, saying they signed on for some Brock's training, and they are not through yet. Ash and the gang laugh, saying the Professor's research is training, and they head off, leaving Brock saddened. Meanwhile, in a field somewhere offshore, a red helicopter lands. Several Team Magma Grunts leap out smiling. Ash and friends arrive at a large tunnel and decide to investigate it. As they reach the end, a small door blocks the path. Max walks up to it and knocks, but no one answers. He shrugs and checks the knob, exclaiming that it's unlocked. Ash opens the door and the group heads inside. A Pokémon desk and chair are present, along with plants and a bookshelf; this is obviously a secret base. Max pulls a book off the shelf and begins to read. Suddenly a small boy and his Nincada rush in screaming. He yells at the group, saying they are intruding. Ash is shocked and explains that they stumbled by. The boy becomes enraged, screaming that his secret base isn't secret anymore.
He tells Nincada to attack, and the group rushes out of the base scared stiff. Team Rocket is hiding behind a trap against the wall. Meowth and James comment that the kid's Nincada is pretty strong and Jessie says it should be easy to steal. Outside, Ash and his friends take a breather. Professor Birch explains that secret bases are all the rage now, and trainers put them up everywhere as kind of their own little hideaway. Ash and friends understand, then he boy begins to clean up, when a knock comes at the door. He opens it to find no one there and shrugs. He turns around, but Team Rocket appears at the door. They greet him, then happily pull out their Poké Balls. The kid screams and seconds later, he rushes from the base. Inside, Team Rocket laughs as they watch him go. Meowth is perched on top of Nincada grinning. Somewhere in the ocean, a sub surfaces. Several Team Aqua Grunts leap out in scuba gear and dive under the water.
Back in the base, Jessie has Cascoon tie Nincada up. She then hugs it, praising it for a good job. Meowth and James sigh and begin to play with the boy's computer. James contacts the boss and is surprised he actually answers! He flies back and Jessie steps up. They all crowd around as he asks them what their progress in Hoenn is. They say it's going great and they even have their own Rocket Base now. The three show off the secret base, but Giovanni says that it looks like a kid's room. He asks if they have taken care of the other teams yet, but James says they are working on it. Meowth says Team Rocket will be the only team in Hoenn soon, and Giovanni angrily hangs up. The three sigh, knowing they need to get working. Jessie then comments that they have a base and a Pokémon now, so they should be in control in no time, and they all cheer. Outside, Ash and his friends head away from the cave. May suddenly notices the boy from before sulking on a rock. They approach him and apologize while introducing themselves.
The boy's name is Keanu, and he tells them to go away. Max asks where Nincada is and the boy begins to cry. He tells them that his base and his Pokémon were stolen from him. Back in the base, Jessie makes a string leash and ties it to Nincada. She then has it start digging, exclaiming that they need to make this base a whole lot bigger if they want to fit Team Rocket grunts inside. Suddenly the door swings open and Team Magma spills into the room. Team Rocket recognizes them from before and Jessie yells, saying this is their base. The Magma Grunt Leader informs them that they are in the way, and this base belongs to them now. Team Rocket refuses and starts their motto, but the Grunt's release several Mightyena gang. Jessie and James stop their motto and freak out, and rush from the base. With them gone, the Grunts bring in a large drill. It crushes Keanu's stuff as it makes its way to the back of the room. The drill begins to drill a hole in the back wall, making a tunnel. The Grunt Leader looks on, then motions for them to head inside. Outside, Ash and friends sit down listening to Keanu's horrid tale of how a team stormed his base and overtook him.
Max and Ash are a little confused how this all happened, but they understand. The boy begins to mope, talking about all the time and effort he and Nincada put into the base, and how much he misses his Pokémon. This enrages May. She stands up and begins to yell, saying that instead of moping around he should be trying to get it back. Ash and friends are a little embarrassed, and Max comments that May is usually the one moping when her Pokémon are caught. She falls down, embarrassed. Ash then steps up, exclaiming that he will help Keanu reclaim his base and get Nincada back. Keanu is happy and thanks him. The drill makes it into a large cavern with a huge shrine in the middle. The Grunt pushes a button and two missiles shoot into the ceiling, but turn into lights at the top. He then tells the others to move quickly. Team Rocket watches from behind some rocks, wondering what's going on. Jessie exclaims that whatever it is, it must be important, and they should be quiet. She then suggests that the take whatever relics Team Magma finds. Team Magma rides the drill down to a small pedestal with two holes in it. He tells the others to search the area. Up above, Jessie has Cascoon make a rope out of string so they can scale down the shrine to where the Team Magma members are.
James and Meowth aren't so sure about this. Back at the secret base, Keanu realizes that all his stuff is destroyed and becomes enraged. They all notice the tunnel, and Ash says they won't get away with this. At the shrine, Team Magma is doing an extensive search. The leader suddenly gets a call from his superior, saying Team Aqua may be lurking nearby. He walks toward the water. Ash and friends enter and see what's going on. Team Rocket is also trying to get inside. Team Aqua has now made it, and leap from the water. No sooner then this happens does the Magma Leader order a Shadow Ball from Mightyena. The female Aqua Leader orders a Hydro Pump from her Carvanha, blocking the attack. The two stare each other down, then the Aqua Leader orders her Grunts into the shrine.
She tells the Team Magma Leader that the world is better off as an ocean, but the Magma Leader disagrees, saying the world should be all land. Ash and the gang are confused, but Professor Birch explains that these two teams have been fighting in Hoenn for ages, each with a different view on how the world should be. Keanu then says that these aren't the people who attacked him, and the ones that did had a Meowth. Down below, the two continue to argue, explaining to each other their viewpoints. They then begin to relay back and forth what their respective bosses are saying to them. It ends with each leader calling their Grunts back for a battle. After a stare down, each leader recalls their Pokémon, saying it isn't worth their time. They have both collected enough information to leave. The Aqua members dive away as the Magma members fly back up on their drill, confusing everyone. Ash and co come out of hiding to see Team Rocket cheering at how big their new base will be. Ash notices Nincada and they call down to the Rockets, saying they won't get away. May has Silcoon make a rope down, and Ash tells Keanu they have to slide down.
Keanu is a little scared, but Ash slides down with no problem. May begins to explain to Keanu that he has to be assertive is he wants to get his Pokémon back, and after a few seconds of pep talking, he agrees. Ash and the Rockets argue for a bit, when suddenly Keanu comes crashing down on top of Team Rocket! Nincada flies up, and Pikachu uses Iron Tail to break the string leash. When Nincada lands, Keanu has it use Secret Power, sending Team Rocket blasting off again. Outside the cave, Keanu thanks Ash and friends for everything. Ash compliments him on the great Pokémon he is raising, and scans it with the dex. After some more talk about Keanu wanting to challenge the Gym Leaders, he and Ash shake hands. May is happy to see they are friends, and the scene then rises into the sunset.
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