Ash and co. are training for the rematch at the Dewford Gym by running along the side of the beach. Brock notices something weird. Everyone stops their running. They see a guy climbing the cliff. The guy is Professor Birch. He is examining a Wingull's nest. A Wingull flies down it its nest and pecks on Professor Birch. Professor Birch falls and lands on a Loudred. The Loudred gets angry with Professor Birch, and it uses Hyper Voice to knock Professor Birch off the cliff. Ash and co. crowd around Professor Birch.

Professor Birch is happy that Brock managed to join with the group. Ash asks Professor Birch what he is doing here. Professor Birch tells him that he is examining the Pokémon. He points to the Wingull and their nests. May thinks that climbing the cliffs are a bit dangerous, but Max reassures her that Professor Birch is famous for doing extreme missions. Team Rocket watches Professor Birch and the others from behind a few rocks. Meowth thinks that Professor Birch can lead them to lots of rare Pokémon since he is a Pokémon researcher. Ash tells Professor Birch that he is training for a rematch at the Dewford Gym, and May tells the professor that she has decided to participate in Pokémon contests. Professor Birch has decided to stick around for a bit. Ash and co. decide to hang out with the professor.

A red plane has just landed in a part of the forest. The plane belongs to Team Magma. A few members of Team Magma walk out. Ash and co. approach a cave. Professor Birch states that the cave may have some Golbat in it. Max hopes the Golbat will come out. Suddenly, they come to a dead end. At the end is a door. Max knocks on the door, but no one answers it. Then Max notices the door is unlocked. They walk inside. Behind the door is a secret base. Max finds lots of Pokémon books about strategies and battling. Suddenly, a boy walks in with his Nincada. He isn't too happy to see Ash and co. The boy yells at them for trespassing, and he forces them out. Team Rocket have disguised themselves in the cave. They notice that Ash and co. have stumbled upon something.

Ash and co. realize that the boy has a big temper. Professor Birch assumes that he is a Pokémon trainer. They decide to move on to the next cave. The boy closes the door. Another knock is then sounded on the door. Team Rocket appears. They hijack his place and steal his Nincada. The boy runs out screaming.

A large submarine belonging to Team Aqua surfaces the water. A few members of Team Aqua dive into the water. Cascoon has tied Nincada to the wall with its String Shot attack. Jessie wants Nincada to build them a lot of secret bases. She tells her "Silcoon" that it is very cute and strong. Meowth and James know that it is a Cascoon though. James turns on the computer screen and Giovanni appears. Giovanni wants to know why Jessie, James, and Meowth have disturbed him. Jessie tells him that they made a secret base. Giovanni thinks it's a kids room. Jessie, James, and Meowth promise Giovanni that they will remodel it and make it the best Team Rocket base ever. Giovanni says okay, and then he signs off.

Ash and co. have just come out of a cave. They saw a lot of Golbat in the cave. May spots the boy sitting on a rock. Ash and co. walk up to the boy. Ash introduces himself to him. The boy's name is Kianu. His Nincada was stolen. Meanwhile, Jessie is forcing Nincada to dig through the wall. James and Meowth are busy remodeling the whole place for Giovanni. Suddenly, Team Magma barges in the secret base. Team Rocket remembers them from the Pokémon Center. Team Rocket introduces themselves to Team Magma with their motto. Team Magma sends out their Mightyena. They force Team Rocket out of the base. Then the Team Magma leader orders a machine in the secret base. The machine blasts a hole in the wall making a pathway. Then they proceed inside the wall.

Kianu tells Ash and co. that he loves Pokémon, but he was never able to win a battle before. Because he has never won a battle before, he hates battling. So, Kianu had his Nincada dig out the secret base, a place where they could train. May yells at Kianu that he has to battle with Pokémon and train them instead of feeling so down with himself. Ash wants to help Kianu train. Kianu thanks Ash for his offer.

Team Magma have blasted their way through the wall into another dark room. A large pyramid lies in the middle of the room. Their machine fires two missiles each lighting up the pyramid. Their leader believes that he is in the Cave of Origin. Team Rocket is hiding behind some rocks. They notice that Team Magma is looking for something valuable, so they plan on finding it first. Team Magma uses their machine to go down to the pyramid. The leader sees a stone with two holes in it. He tells his squad to search the area for some valuables. Jessie gets her Cascoon to make some thread for them, so that they can climb down.

When Ash and co. return to the secret base, they find everything destroyed. Kianu can't find Nincada anywhere in the secret base. Professor Birch notices the giant hole in the wall. They decide to follow it because that will hopefully lead them to some answers.

Meanwhile, the Team Magma squad is searching the area. They haven't found anything yet. Ash and co. have finally made it to the room. Ash notices a big building standing in the middle of the room.

Suddenly, Team Aqua approaches the room from underwater. The Team Magma leader has been expecting them. His Mightyena uses Shadow Ball, but Team Aqua's Carvanha counters the attack with Hydro Pump. The Team Aqua leader tells her squad to go complete their mission. Then the two leaders communicate with each other. They both are seeking power in these ruins. They begin to talk about the Indigo and Rose orbs, and which team can control them. Team Magma is seeking the power of the land, while Team Aqua is seeking the power of the sea. Team Magma's people reports back to their leader that they couldn't find anything. Team Aqua also reports back to their leader that nothing was found. Both troops pull out.

Team Rocket comes out and cheers now that Team Magma and Team Aqua are gone. They continue along with their plans. Ash and co. interrupts Team Rocket's plans. They demand for Nincada back. May's Silcoon uses String Shot. The thread attaches to one of the poles of the building. Ash tells Kianu to come with him to save Nincada. Ash slides down the thread and faces Team Rocket. Team Rocket refuses to give Nincada back. Kianu then slides down the thread and knocks into Team Rocket. Jessie accidently lets go of Nincada. Pikachu then uses Iron Tail to cut the thread that was trapping Nincada. Now that Nincada is safe, Nincada uses Hidden Power on Team Rocket. Team Rocket blasts out of the cave.

Back outside of the cave, Ash and co. congratulate Kianu for saving Nincada and defeating Team Rocket. Then Ash looks up Nincada in his Pokédex. Kianu wants Ash to battle him once he gets a lot stronger. Ash agrees to the battle. Now Ash must continue his training for his rematch at the Dewford Gym.

English Official Summary

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.

French Official Summary

Sacha et ses amis rencontrent le Professeur Seko et l’accompagnent dans ses recherches à l’intérieur de plusieurs grottes qui se trouvent dans les environs. Dans l’une d’entre elles, ils découvrent une salle secrète, occupée par un jeune garçon qui les chasse rapidement de ce qu’il appelle sa « base secrète ». Sur les traces de Sacha et de ses amis, la Team Rocket ne répond pas aussi poliment à la demande du garçon. Au lieu de ça, ils le jettent dehors et s’emparent de la base et du Ningale du jeune homme ! L’affaire se complique lorsque deux factions rivales de la région de Hoenn : la Team Aqua et la Team Magma, s’introduisent dans cette même grotte, qu’ils pensent être la légendaire Grotte Origine...

German Official Summary

Ash und sein Team trainieren am Strand. Kurz darauf entdecken sie Professor Birk, der Nachforschungen über Wingulls anstellt.

Italian Official Summary

Ash e la sua squadra si allenano sulla spiaggia. Presto scoprono che il Prof. Birch sta compiendo delle ricerche sui Wingull proprio in quella zona.

Portuguese Official Summary

Ash e os outros se reúnem com o Professor Birch para um dia de exploração e acabam no meio de um confronto vilanesco!

Spanish Latin America Official Summary

Ash y los otros se reúnen con el Profesor Birch para un día de exploración y terminan en medio de una villanesca confrontación.

Spanish Official Summary

Ash y sus amigos quedan con el Profesor Abedul y le acompañan para investigar unas cuevas cercanas. Dentro de una de ellas, descubren una sala oculta ocupada por un joven que los echa enseguida de lo que él denomina su “base secreta”. Muy cerca de Ash y sus amigos, el Team Rocket no responde con tanta educación a la petición del chico, le echa de ahí y se queda con la base y el Nincada del chico. Todo se complica cuando las dos facciones rivales de Hoenn, el Equipo Aqua y el Equipo Magma, se infiltran en esa misma cueva pensando que se trata de la legendaria Cueva Ancestral.

English Great Britian Official Summary

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.

Russian Official Summary

Эш и его друзья встречают профессора Бёрча и отправляются вместе с ним в поход по пещерам. Внутри одной из них они  обнаруживают тайную комнату некоего мальчика Кину, который прогоняет их из своей, так называемой, "секретной базы". Следуя по пятам Эша и его друзей, Команда Р долго не церемонится с Кину, и выкидывает его из тайного убежища. Они занимают штаб Команды Кину для себя. Ситуация осложняется, когда две враждующие группы региона Хоенн, Команда Аква и Команда Магма, также оказываются в этой пещере, которая считается священной. Когда они понимают, что ошибаются, то оставляют секретное убежище Команде Р - но не на долго! Наши герои уже спешат их остановить и вернуть Кину его тайное убежище.

Dutch Official Summary

Ash en de anderen ontmoeten Professor Birch om een dagje met hem op onderzoek uit te gaan, maar belanden middenin een doortrapte confrontatie!

Danish Official Summary

Ash og de andre mødes med professor Birch for at gå på opdagelse, men ender midt i et sammenstød af skurke!

Swedish Official Summary

Ash och de andra träffar professor Birch för att tillsammans tillbringa dagen med utforskning, men det hela slutar med en skurkaktig sammandrabbning!