At the end of the previous episode, Pikachu’s Thunderbolt had blasted off Team Rocket one way, and Pikachu, Ash, and friends the other way. Ash and friends are now floating in the ocean, hanging onto logs, wondering what to do now. Suddenly, a giant submarine surfaces right under them! They are now riding it, and conclude that someone has rescued them. They call out towards the submarine’s conning tower, trying to attract someone’s attention, when to their surprise, a Team Magma member rises from it! They hide as the member, who turns out to be our old friend Harland, looks through his binoculars towards their destination up ahead. (Apparently, he hadn’t heard their calls, but was coming up on his own anyway.) From their hiding place out of Harland’s view, Ash & friends recognize him and realize the sub belongs to Team Magma. They watch as the sub heads for an opening in a much larger ship ahead.

Once the sub reaches the dock inside, two crewmembers acknowledge their boss, Maxie, who is waiting for them. Maxie notices Ash and friends, now exposed to everyone’s sight, frantically looking for another place to hide. After forcing them on deck with their hands raised, the team then encircles Ash and friends, and they use two of their Mightyena to guard the prisoners. While they talk, another female Magma member slips unnoticed out of the sub, and heads off another way. Maxie and Harland confer briefly about the possibility of Team Aqua being nearby, then the scene switches to the mysterious female Magma member. She approaches two male grunts that are guarding a door. Two well-placed punches later, both grunts are out cold. The woman then pulls back her hood to reveal that she is actually Tactical Commander Isabel of Team Aqua. She goes into the door, entering a room that houses Kyogre’s containment chamber. Yes, Team Magma has captured Kyogre, and Team Aqua wants it. Isabel punches a code into the control panel for the chamber, and a rush of steam comes from several vents inside it.

Meanwhile, Team Magma has taken their captives to Maxie’s office on the ship. Maxie tells Ash and friends to sit down so they can talk, but Ash angrily refuses, saying he’d rather stand. In response, the Mightyena growl fiercely at the captives. This frightens May and Max, and the group finally sits down. Ash promptly yells at Maxie, the Mightyena growl again, and May calls Ash’s name in a scared voice, meaning he should calm down. Harland jumps in, saying nobody talks to his boss that way, but Maxie calms him down. Maxie goes on to explain about their plans to increase the earth’s land, and surprises Ash and friends by saying they plan to awaken the legendary Groudon. They have currently captured Kyogre, which Team Aqua is after, and they know that Team Aqua has Groudon, so they want to swap prisoners. The Blue Orb rises from Maxie’s desk, and he explains that whoever holds the orb can control Groudon, giving him ultimate power. Team Magma plans to use that power to increase the world’s land and finally defeat Team Aqua.

Meanwhile, Isabel has now managed to increase the humidity in Kyogre’s chamber to enough of a level that it can be revived. Alarm sirens sound in that room, and even as far up as Maxie’s office. Everyone is startled, and Maxie hits the button for the intercom on his desk. A Magma grunt’s voice on the intercom explains the situation. Kyogre has now fully awakened, and Isabel calls out for it to break free. It breaks its bonds without much difficulty, but can’t break its muzzle. Regardless, it plunges through the wall and into the ocean, causing the ship to tilt violently to one side. A red-haired male Magma grunt confronts Isabel on the ship’s deck. She removes her Magma disguise, revealing her Team Aqua wetsuit, 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 (apparently from Kyogre) 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. Harland has the three Mightyena who had been guarding them try to stop Pikachu, but Pikachu jumps from one Mightyena’s head to the other, and finally to the orb. Pikachu lands, having successfully caught it. Suddenly, a quick cutscene shows an opening eye and a growl, and the Blue Orb starts to glow and absorb itself into Pikachu’s body! Pikachu writhes in pain briefly, and at Maxie’s suggestion, Harland 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 Harland pulls out a Pokeball, but just then, another explosion hits the wall behind him. Ash and friends take that opportunity to escape. Harland helps his boss up, and Maxie says they’ve got to get that Pikachu back.

Not far away, Team Aqua’s sub surfaces, as Isabel 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 releases a Hyper Beam at Team Aqua’s ship. On that ship, the red-haired Magma member pulls out a Pokeball, noting that the situation has now turned drastic. But then he notices Ash and 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 Harland’s Mightyena. Harland gloats, having cornered Ash.

May, Max, and Brock now surface and wonder where Ash is. Then, they notice that he’s been captured! Harland and his two Mightyena are bringing Ash onto Team Magma’s helicopter. Harland confers with a teammate, while the mysterious red-headed grunt listens. The helicopter takes off from Team Magma’s ship as Archie watches from his sub. With the Red Orb still in hand, Archie promptly has Kyogre finish off the ship, so it is sure to sink. This creates a powerful downward current that pushes May, Max, and Brock deeper into the water, but…something…is following them.

The scene then switches to show Team Rocket, lying on a beach with the wind knocked out of them. This is where they had landed following the previous episode’s blastoff. They recognize Team Magma’s helicopter flying overhead, and wonder what they’re up to. Meanwhile, out in the ocean, a red Gyarados surfaces, carrying an unconscious May, Max, and Brock. They awaken, and May and Max promptly get scared when they realize they’re on a Gyarados, but Brock recognizes it as Lance’s.

While this is going on, it’s time for the big meeting between Teams Aqua and Magma. Magma’s helicopter lands, and the team gets out. Archie reveals that he has two Team Magma hostages, and offers to trade them for the Blue Orb. Team Rocket are watching this from not far off, and are 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 catch Groudon and Kyogre to give to the Boss (as if that’ll happen).

Meanwhile, Ash and Pikachu are still trapped in Team Magma’s helicopter, and guarded by several grunts outside. Pikachu is still in pain from having absorbed the Blue Orb. Suddenly, it glows with those red markings again and breaks free of Ash’s grip. It then basically goes insane, letting out massive bursts of electricity everywhere, including one that just misses Ash, before finally fainting from the strain. Worried, Ash picks it up, but then notices the red-haired Magma member from earlier at the door. 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 explains what happened to Pikachu. Lance doesn’t think Pikachu is in life-threatening danger, so he reassures Ash and explains more about what’s going on.

By now, May and Max have calmed down about the Gyarados, since Brock has been explaining to them about who Lance is and how he and Ash know him, as Gyarados takes them to the island where everyone is. Another scene-switch shows Team Rocket observing Team Aqua’s sub. They know from what they overheard that Team Aqua is keeping Groudon and Kyogre captive there. Two Aqua guards with their Crawdaunt make their rounds, but after they have gone by one of the storage containers, part of the wall falls down, and Team Rocket emerges. They’d disguised themselves with a fake wall like the kind of thing some ninja trainers in Ruby and Sapphire use to blend in with their surroundings. They tiptoe off, and come to a control panel and monitor that shows where Kyogre is being held now. Jessie pulls out a bazooka, and Meowth enters a password on the keyboard, but it doesn’t work. Jessie and James tease Meowth as he presses random buttons, eventually shutting down the computer. Jessie and Meowth argue, and Wobbuffet tries a button that causes an explosion. The door Team Rocket wanted opens, and they rejoice, but are stopped short by the Aqua guards and their Crawdaunt.

Back at the showdown between Archie and Maxie, Isabel receives a report on her radio about Team Rocket, and Archie blames Team Magma for the intrusion. Maxie denies any involvement. The scene switches to May, Max, and Brock running towards the action. A storm quickly starts, and they decide to hurry.

Meanwhile, James sends out Cacnea to deal with the Aqua guards’ 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 fires a net from her bazooka that envelops Kyogre, and she then presses a button that electrifies the net, attempting to weaken the Water-type. It seems that her voltage wasn’t nearly high enough though, since the electricity merely alerted Kyogre. It jumps out of the water, sending the electrified net back onto Team Rocket and blasting them off. The explosion causes a fire in Kyogre’s containment chamber.

Still captive in Team Magma’s helicopter, Ash is holding Pikachu, trying desperately to calm it down as it goes insane again, letting out bolts of electricity everywhere. Ash is getting hurt, but won’t let go of Pikachu this time. The narrator then sets the stage for the next episode, explaining the danger everyone is in if both Kyogre and Groudon are awakened (as Kyogre has been already), and the episode ends on that note, preparing for part 2.

Thanks To Geodude For Writing this for us