The episode opens up with Brock helping Ash and his team train on the beach. They soon discover that Professor Birch is in the area doing research on Wingull. Professor Birch offers for Ash and the gang to join him in his research. They agree and soon come across a hidden doorway. They discover it is unlocked and it turns out to be someone's Secret Base. The owner of the base arrives and kicks them all out. They rush away before the boy's Nincada can attack them. Team Rocket sees all this and after Ash and company leave, they force the boy out of his base and claim both the base and his Nincada as their own. They contact their boss to gloat about their accomplishment only to be told that they should be doing a lot more.
Outside, our heroes run into the boy again. The gang introduces themselves, and find out the boy's name is Keanu. They listen to his story and convince him, with their help, to go back and reclaim his base. In the meantime, some Team Magma grunts were dropped off nearby via helicopter and some Team Aqua grunts are somewhere near in a submarine. The Team Magma grunts reach the base and claim it for themselves using their Mightyena. Team Rocket then rushes from the base and the Magma grunts begin to drill. Eventually, the drilling leads to a secret cavern with some sort of shrine in it. Team Rocket is spying on them at this point, hoping to steal whatever it is Team Magma finds.
Team Aqua suddenly arrives and a short battle and argument ensues between the rivals. Their bosses call them both back, claiming to have all the needed information. Team Rocket is marveling at how big their new base is when Ash and Keanu slide down a rope made by May's Silcoon to reclaim the base. Team Rocket is defeated again and the show ends with Keanu and Ash shaking hands as friends.
The group 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 followed by the Pokémon behind them, while 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. Birch loses his grip and falls down, landing on none other than 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 burrows away. Ash and his friends approach and greet him.
Professor Birch suggests they catch up, so everyone sits amongst the rocks. Brock thanks the Professor for helping him reach Ash and the others. Ash asks Professor Birch what he is doing on Dewford Island, 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 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 that Ash is battling through the Gyms while May has decided to compete in Pokémon 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 that his scheduled training has been set back. Ash and the gang laugh, saying the Professor's research is training, and they head off, leaving Brock saddened. Meanwhile, in a field somewhere, a red helicopter lands and several Team Magma Grunts emerge from the aircraft.
Ash and friends later arrive at a large tunnel and decide to investigate it. They, however, come to a dead end blocked by a wooden door. 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. Max pulls a book off the shelf and begins to read. Suddenly a small boy and his Nincada rush in demanding answers. He yells at the group, saying they are intruding. Ash is shocked and explains that they stumbled by. The boy still enraged, refused to listen to reason, 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 then emerge from their rock camouflage. 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 suggests that they explore another cave, and the others agrees. Back in the base, the boy begins to clean up, when a knock comes at the door. He opens it to find no one there. He turns around as 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 flee. Meowth is perched on top of Nincada grinning. Meanwhile, a Team Aqua submarine bursts from the water. Shelly and several Team Aqua Grunts all in scuba gear take a moment to examine the Dewford coast before beginning their swim towards the island.
Back in the base, Jessie has Cascoon use String Shot to tie Nincada up. She praises her "Silcoon" for a good job, as Meowth and James wonder when they will break the news to Jessie that it actually a Cascoon. James contacts Giovanni on the computer and is surprised he actually answers. The pair fall backwards as 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, so the three admit they will renovate it. He asks if they have taken care of the other teams yet, but James says they are working on it. Meowth declares that Team Rocket will be the only villainous team in Hoenn soon. Giovanni demands they report back to him once the base has been renovated and abruptly hangs up. The three sigh in relief knowing they need to get working to get their promotions. 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 another cave. May suddenly notices the boy from before sulking on a rock. They approach him and apologize while introducing themselves. The boy reveals that he is named Keanu. Max asks where Nincada is and Keanu begins to cry. He tells them that his base and his Pokémon were stolen from him.
Later, Jessie has Nincada by a leash and orders 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 at them for trespassing. The Magma Grunt Leader, Tabitha 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 rush from the base in fear. With them gone, the Grunts bring in a large boring machine. It crushes Keanu's stuff as it makes its way to the back of the room and tunnels through the rock. Tabitha looks on, then motions for the grunts to head inside.
Meanwhile, Keanu reveals that he has never won a battle before, which surprises Max and Ash, and built the base in order to train with his Nincada. This enrages May. She stands up and begins to yell, saying that after he catches a Pokémon, he is supposed to train it and battle it with other opponents, not hide away in a base. Ash and friends are a little embarrassed, and Max comments that May isn't one to talk about Pokémon training. 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.
Team Magma have broken through to an ancient shrine. Tabitha gives the signal and two missiles launch from the boring machine and into the cavern ceiling. The missiles open up into two bright spotlights, helping to illuminate the dark cavern. Tabitha declares that they have finally made it to the Cave of Origin and orders 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 she 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 to the shrine.
Keanu returns to his Secret Base and is enraged to find all of his stuff destroyed. They all notice the tunnel, and Ash says the culprits won't get away with this. At the shrine, Team Magma is undertaking an extensive search for "G". As Ash and the others arrive at the ancient site, so does Team Aqua. Tabitha orders his Mightyena to attack with Shadow Ball, but Shelly has her Carvanha block it with a Hydro Pump. The two stare each other down, then the Aqua Leader orders her Grunts into the shrine. The team commanders get into a heated debate. Shelly declares that the world is better off as an ocean, but Tabitha disagrees, replying the world should be all land. Ash and the gang are confused, but Professor Birch explains that these two teams are notorious troublemakers. Brock queries if either team took Nincada, but Keanu says no, and adds the ones that did had a Meowth. Meanwhile, Shelly insists that Team Magma cannot be trusted with the Blue Orb. The two commanders soon receive word that neither "G" or "K" could be located. A Team Aqua Grunt also reports that the ancient site isn’t the Cave of Origin, but simply an ancient shrine of worship. The two commanders decide to settle their difference of opinions with a battle, and call back their grunts to assist. 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 Team Magma fly back up on their drill, confusing everyone.
Ash and the others 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 hesitant, but Ash slides down with no problem. May begins to explain to Keanu that he has to be assertive if 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 Hidden Power, sending Team Rocket blasting off. 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 Pokédex. After some more talk about Keanu wanting to challenge the Gym Leaders, he and Ash shake hands. May is just happy to see they are friends.