The kids are floating on logs at sea when a red submarine appears beneath them, belonging to Team Magma. At the floating Magma base, the kids are taken into custody. Team Magma Leader Maxie explains to them about how he has the Blue Orb in his possession, allowing him to control Groudon. Unfortunately, the Legendary Pokémon they currently have in their possession is Kyogre.
A disguised Shelly of Team Aqua sneaks away and unlocks Kyogre, setting off an alarm. Kyogre awakens and busts out of the floating base, causing it to begin sinking. In the chaos, the kids try to grab the orb, and Pikachu accidentally absorbs it and goes berserk.
Ash is separated from his friends and attacked by a Team Magma member. He meets what appears to be another member of Team Magma—but it's really Lance of the Elite Four in disguise! Lance has also sent his red Gyarados to go help Ash's friends.
Both Teams Magma and Aqua end up on Monsu Island, along with Team Rocket, who wants to steal both Legendary Pokémon. Of course, it's no good, as Kyogre is under the control of the Red Orb, which is currently in Team Aqua's possession...
Ash and his friends find themselves stranded in the middle of the ocean after Team Rocket tried to steal Pikachu at the end of the previous episode. Suddenly, a giant red submarine surfaces right under them. They call out towards the submarine's conning tower, trying to attract someone's attention, when to their surprise, a Team Magma Grunt rises from it. The group hides as the grunt, who turns out to be Tabitha, scans the surrounds with his binoculars. They watch as the sub heads for an opening in a much larger ship ahead, which May realizes to be Team Magma's base. Once the sub reaches the dock inside, two crew members acknowledge their boss, Maxie, who is waiting for them. Maxie immediately notices Ash and his friends as they frantically look for another place to hide. After forcing them on deck with their hands raised, Team Magma and their snarling Mightyena encircle the group. Maxie officially introduces himself and orders them to stay out of his plans.
While Maxie and Tabitha confer briefly about the possibility of Team Aqua being nearby, Shelly of Team Aqua, disguised in Team Magma apparel, emerges from the docked submarine. She approaches two male grunts that are guarding a door. Two well-placed punches later and both grunts are out cold. Shelly enters a room that houses Kyogre held in a containment chamber. She punches a code into the chamber’s control panel, helping to awaken Kyogre.
In his office, Maxie tells Ash and his friends to sit down so they can talk, but Ash angrily refuses, saying he'd rather stand. In response, a Mightyena growls fiercely at the captives, frightening May and Max, and the group finally sits down. Ash accuses Team Magma of being selfish and wanting to control ancient Pokémon. Tabitha jumps in, saying nobody talks to his boss that way, but Maxie calms him down. Maxie corrects Ash as he explains that Team Magma want to increase the earth's land mass, and awakening the Legendary Pokémon Groudon is part of the process. They have currently captured a Kyogre, which Team Aqua is after, and they know that Team Aqua has a Groudon, so they want to swap prisoners on nearby Monsu Island. The Blue Orb rises from Maxie's desk, and he explains that whoever holds the orb can control a Groudon, giving them ultimate power. As Maxie orders Tabitha to lock Ash and his friends up, an alarm sounds as Shelly revives Kyogre. The Legendary breaks free of its restraints and crashes through Team Magma’s hull, escaping into the ocean. Shelly reports to her superiors that the mission has been a success. Lance, disguised as a Magma grunt while he undertakes his latest Pokémon G-Men mission, confronts Shelly on the ship's deck. She removes her Magma disguise, revealing her Team Aqua wet suit, and leaps overboard into the water.
Back in Maxie's office, scrambled intercom reports of the confusion related to Kyogre's escape are still pouring in. Suddenly, a blast knocks Maxie down and sends the Blue Orb flying. Brock exclaims that now's their chance to get it, so Ash gets Pikachu to do so. Tabitha orders three Mightyena to intervene, but Pikachu jumps from one Mightyena's head to the other, and finally catches the orb. Unexpectedly the Blue Orb begins pulsing with a red light and absorbs itself into Pikachu's body. Pikachu writhes in pain briefly, and at Maxie's suggestion, Tabitha takes the opportunity to have the Mightyena attack. Hearing them, a possessed Pikachu turns around and defeats all three with a supercharged Thunderbolt. Pikachu sways back and forth from the strain, and Tabitha pulls out a Poké Ball, but just then, another explosion hits the wall behind him. Ash and his friends take that opportunity to escape. Tabitha helps his boss up, and Maxie says they've got to get that Pikachu back.
Not far away, Team Aqua's sub surfaces, as Shelly reports to Aqua Leader Archie that the operation to release Kyogre was successful. Archie holds up the Red Orb, and it glows, summoning Kyogre, who launches a Hyper Beam at Team Magma's ship. On that ship, Lance pulls out a Poké Ball, noting that the situation has now turned drastic. But then he notices Ash and his friends on the deck below him, recognizing Ash and wondering what he's doing mixed up in all this. Brock says their only chance is to abandon ship, so he dives into the water along with May and Max. Ash and Pikachu are about to follow when they're suddenly blindsided by one of Tabitha's Mightyena. Tabitha gloats, having cornered Ash. As they resurface, Ash’s friends realize Ash is missing and watch as Tabitha forces Ash aboard a waiting helicopter. Lance, still in disguise, also hops on the craft as it sets off for Monsu Island. With the Red Orb still in hand, Archie promptly has Kyogre finish off Team Magma’s ship, so it is sure to sink. This creates a powerful downward current that pushes May, Max, and Brock deeper into the water. The trio are soon saved by a Red Gyarados, and Brock quickly recognizes it as Lance’s.
Team Rocket find themselves lying on Monsu Island’s shore with the wind knocked out of them from their earlier blast off. They recognize Team Magma's helicopter flying overhead, and wonder what they're up to. Team Aqua and Team Magma finally come face-to-face for their arranged swap. Archie reveals that he has two Team Magma hostages, and offers to trade them for the Blue Orb. Team Rocket is watching this from not far off, and is stunned at the mentions of Groudon and Kyogre in the negotiations. After some more discussion, Archie reveals to Maxie that he already has the Red Orb and can control Kyogre, and that he'll be unstoppable if he can get the Blue Orb as well. Team Rocket comments on this, and decide to steal Groudon and Kyogre to give to the Boss.
Meanwhile, Ash and Pikachu are still trapped in Team Magma's helicopter, and guarded by several grunts outside. Pikachu continues to writhe from the pain of absorbing the Blue Orb and becomes increasingly hostile. The red-haired Magma member from earlier enters the room. Ash is angry at first, but the Magma member removes his hood to reveal that he's Lance. He quietly fills Ash in on the situation, and Ash informs him that Pikachu bonded with the Blue Orb. Lance doesn't think Pikachu is in life-threatening danger, so he reassures Ash that he will do his best to help out.
The Rocket trio set their sights on infiltrating Team Aqua's sub in the hopes of nabbing Groudon or Kyogre. Using a fake wall, they slip by two patrolling Aqua guards and their Crawdaunt, and soon locate Kyogre's storage cell. Jessie pulls out a bazooka, and Meowth enters a password on the keyboard, but it doesn't work. Meowth resorts pressing random buttons, eventually shutting down the computer. Jessie and Meowth argue, and Wobbuffet tries a button that causes an explosion and incidentally opens the door. Team Rocket rejoice, but are stopped short by the Aqua guards and their Crawdaunt. Shelly receives word of the intruders, and Archie is quick to point the finger at Team Magma. Though Maxie denies any involvement. James sends out Cacnea to deal with the two Crawdaunt. A single Pin Missile is all that's necessary to let Team Rocket go by, and they quickly approach Kyogre's tank. Jessie ensnares Kyogre in an electrified net, attempting to weaken the Water-type. However, Kyogre awakens in a rage. As Kyogre jumps out of the cargo hold, it sends the electrified net back onto Team Rocket and blasts them off. The explosion causes a fire aboard the sub. Meanwhile, Ash desperately tries to hold Pikachu as he goes insane from the surge of the Blue Orb's power.