The gang is seen to be harmed by Pikachu's attack, floating on water. Suddenly, a wave approaches - they are standing on a submarine. They call for help, but they wish they didn't. It is the Team Magma on the submarine. They hide and overhear the leader. Suddenly, they see a giant ship, presumably Team Magma's base. The submarine arrives in the ship and the leader sees the gang. They have been interrogated. The man introduces himself as Maxie - Team Magma's leader. Unusually, he tells them to be in the submarine and not do anything. Tabitha tells Maxie that he saw Team Aqua on the sonar. A woman approaches to a room and pounds the guards. The woman is Team Aqua's member, Shelly.
She enters the room, seeing a giant Pokémon - named Kyogre - tied to a machine. She enters a code, starting releasing it. Maxie tells the gang to sit down. Ash refuses, though Brock convinces him to do so. Ash tells them that he knows they are going to use the Ancient Pokémon for their own uses, so Mightyena growl. Maxie tells them that they want to use the Ancient Pokémon for a better world, unlike Team Aqua. He also states they have an Ancient Pokémon already, with the usage of a Blue Orb. Maxie tells them that Groudon and Kyogre made the world they know today. The Ancient Pokémon they have is Kyogre, but also knows Team Aqua have a Groudon. However, the Blue Orb can control Groudon and a Red Orb - which Team Aqua have - can control Kyogre. They are going to Monsu Island to trade the Pokémon. Maxie tells Tabitha to lock the gang up.
The woman has finished with freeing Kyogre, sounding the alarm. Kyogre destroys the machines and goes out of the ship. A man appears, being impressed of Shelly's capabilities. She undisguised herself and goes away. A crash is heard and the Blue Orb is flown to air. Pikachu and Mightyena go to take it, but Pikachu bounces off their heads and takes the orb. A mark appears on the Orb and it is absorbed into Pikachu. Mightyena go to attack him, but Pikachu has strange marks on his head and attacks them without Ash's order. Maxie and Tabitha fall down, so the gang escapes. Shelly informs the Team Aqua leader - Archie - of her success. Archie uses the Red Orb and Kyogre appears before them. Kyogre uses Hyper Beam on Team Magma's ship. The man is about to send Dragonite, but sees the gang. The man spots Ash.
The gang jumps, but Ash and Pikachu are knocked out, still on the ship. As Ash is going as well, he is being attacked by Tabitha's Mightyena. Brock, May and Max see Ash and Pikachu being taken to Team Magma's plane. Archie spots the destroyed ship, so uses the Orb so that Kyogre destroys it completely. Max, Brock and May are drowning, but a Pokémon goes after them. Team Rocket are seen wonded by Pikachu's attack and see Team Magma's plane passing by. Brock, Max and May are seen rescued by a red Gyarados, so Brock remembers it. Team Magma and Team Aqua come to negotiate. Archie shows some of Maxie's spies to release Groudon. Archies shows the Red Orb, clarifying that they have Kyogre as well. Team Rocket spy on them, being impressed by Team Aqua's capabilities. So, once again, they plan to steal the Pokémon and take them to boss.
Ash's Pikachu is seen to be struggling, but the Blue Orb possesses him. Pikachu attacks everything with Thunderbolt, almost hurting Ash. Pikachu then falls down of exhaustion. The man (who spoke with Shelly) comes and undisguised himself - it is Lance. Lance tells him that he was syping on both Teams and preventing them from miss-usage of Ancient Pokémon. Lance notices that Pikachu absorbed the Orb and cannot control it. Brock told May and Max about Lance and the Gyarados - the Pokémon from Elite Four of Johto. The Gyarados is taking them to Monsu Island. Team Rocket come to the ship to release Kyogre. Meowth is pushing the buttons on the computer, but with no difference. He pushes more, destroying the computer. Soon, some members of Team Aqua arrive to intercept them.
Shelly receives info some intruders came to release the Ancient Pokémon, so Archie accuses Maxie for more sabotage. James sends Cacnea to use Pin Missile, hurting Crawdaunt and Team Aqua. Jessie captures Kyogre and sends a electric attack to damage Kyogre. Kyogre releases itself and the net comes to Team Rocket, electrocuting and blasting them off. Pikachu goes uncontrollable with the power of Blue Orb, attacking everything. Ash holds Pikachu, but very difficult.
The rest of the event follows in next episode.
- This is one of few episodes where Cacnea did not hug James.
- Featured Pokémon: Plusle, Minun, Mudkip, Torchic, Treecko