As Ash continues his training, he, May, Max and Brock encounter Prof. Birch. Meanwhile a boy's Nincada was captured by Team Rocket and it digs a hole to a temple. There they encounter the commanders of the teams they encountered before: Team Magma's Harland and Team Aqua's Isabel. How will this clash of Aqua vs. Magma go down, and can Ash and co. help the boy save his Nincada?
The gang is still training, but Brock spots someone climbing a cliff. It is Prof. Birch - he is studying a Wingull's nest, but it gets attacked, so he lands on a Loudred. The gang meets him again. Birch tells of his research, but then May asks if that isn't dangerous, Max steps in to say that Prof. Birch is known for these studies.
Team Rocket overhears the conversation. Ash proposes to stay with Birch, to which he agrees to. Brock reminds them of training schedule, but everybody says they're going to do tomorrow. A plane arrives on the island, with people dressed in red clothes. Birch takes them to a Golbat cave, but they notice an end with a wooden door. Max opens the door - it was already unlocked.
The gang enters the room, seeing that it is a room where one could live. A boy enters the room, angry when they entered his secret base. He yells, forcing everybody to leave his room. The kid calms down, but someone knocks on the door again, with Team Rocket appearing before him and attacking him. Outside, another group arrives, on a submarine marked as Team Aqua.
Jessie's Cascoon (who Jessie thinks is a Silcoon but James and Meowth now it is a Cascoon) has trapped Nincada. They all contact Giovanni, their boss. Team Rocket lie that they set up a secret base, but Giovanni identifies it as a child's room. The gang leaves the cave where the Golbat have been, but May sees the child from the cave. Nincada digs under Jessie's watch, but some people dressed in red arrive. They are actually the same ones they encountered before in the ruins. The man asks Team Rocket who they are and they recite their motto, but they get attacked by Mightyena.
The men start to dig using a machine. The child, Keanu, starts to explain that he does not like battles (as he always loses) so he built the base in the cave to train with his Nincada. May outrages, yelling at Keanu for not battling his opponents at all. Ash will train Keanu, but if he gets his Nincada back. The men have dug out to another cave with a giant building - it is The Cave of Origin.
Team Rocket plans to take whatever is inside the building and get out. Silcoon made a string rope to get to that building. Meanwhile, Keanu finds his room destroyed. The men have been deployed to search the building, but they spotted some other men from water. The men from Team Aqua arrived, but the men in red are one step ahead. Mightyena uses Shadow Ball, but a Carvanha uses Hydro Pump to negate the attack.
The men identify the others - Team Aqua and Team Magma. Team Aqua enter the building, but Team Magma still operate. The woman from Team Aqua taunts the man from Team Magma, knowing that one has to possess Rose and Indigo Orbs to control the water and land. Both commanders receive info that it is only a shrine, not the Cave of Origin.
Both Teams retreat, making everyone confused of what they were talking about. Team Rocket cheers, as they'll take the treasure from the building. May's Silcoon uses Sting Shot and Ash gets down to the building. Keanu also gets down, but knocks Team Rocket down. Pikachu uses Iron Tail to cut the string on Nincada. Nincada uses Hidden Power and blasts Team Rocket away. The gang supports Keanu and Nincada for the battle.
- The dub version of this episode mistakenly calls Tabitha and Shelly by different names; Harland and Isabel respectively. This was later rectified in later episodes.
- In this episode, the Red and Blue orbs were referred to as the Rose Orb and the Indigo Orb respectively.
- Featured Pokémon: Zigzagoon
- This is the only episode in which Shelly doesn't wear her trademark bandanna.