Team Magma and Team Aqua continue to fight on Monsu Island. The Red Orb, which can control Kyogre, is currently held by the Team Aqua Leader Archie. Archie merges with the orb and now crazed as a result, orders Kyogre to sink the island.
Everyone tries to flee into the ruins on the island, while Lance challenges Kyogre with his Dragonite. Dragonite's Hyper Beam is not strong enough to stop the ancient Pokémon.
Team Rocket still wants to steal Groudon, restrained inside the Team Aqua base. Instead, they are attacked by a possessed Pikachu, who awakens Groudon. The giant Ground-type leaves the base and begins a massive battle with Kyogre, but the two are evenly matched.
The kids find a way to distract Kyogre, which gives Groudon the opportunity to defeat the Water-type. The orbs leave the bodies of Archie and Pikachu, floating up in the air until they merge and then disintegrate. Archie and Pikachu both come back to their senses, while the two Legendary Pokémon retreat back into their ancient slumber.
The episode opens with a recap of the previous episode’s events. After that, it’s back to the Team Magma vs Team Aqua confrontation from the last episode. We see the ocean beginning to get violent, and Shelly informs Archie that Kyogre is free from captivity. Archie summons Kyogre with the Red Orb. Team Magma begins to protest, so Shelly orders Team Aqua to bring out their Pokémon to protect Archie. They send out their Walrein, and Team Magma sends out their Mightyena. As the Pokémon battle it out, Archie makes his escape in some kind of mini-helicopter. Tabitha advises Maxie that they have to stop Archie. Tabitha then barks an order to the still-disguised Lance, who hurries off. Just then, Brock, May, and Max arrive, stopping far enough away and behind some bushes so as not to be seen. They comment with surprise that both teams are present.
Meanwhile, Team Rocket is cowering in fear on a rocky ledge at the shore. From his mini-copter, Archie holds up the orb and summons Kyogre, who appears amid a thunderstorm and a raging ocean. Archie then taunts Maxie about how he will conquer the world. He then states that he intends to drown the island under the ocean. Maxie protests (with seemingly genuine concern) that doing so will put people on the island in danger, including members of Team Aqua. However Archie replies that he doesn't care. Shelly and the rest of Team Aqua become shocked at their leader's willingness to sacrifice their lives. They then start to worry about what will happen. Lance, who is standing next to Maxie, removes his hood and calls up to Archie, warning him to stop before anything worse happens, but Archie ignores him. As Kyogre is wreaking havoc out on the water in response to Archie’s commands, Shelly tells the rest of Team Aqua to recall their Pokémon for their own safety. Tabitha tells Team Magma to do the same. Lance now informs Maxie that Kyogre and Groudon are about to fight, and explains the world-shaking consequences of such a conflict, as Archie laughs maniacally from his mini-chopper. Kyogre’s disturbance causes a tremor that makes the downed Magma helicopter to shift, throwing Ash and Pikachu around. The same tremor throws Lance and Maxie to the ground. Inside, Pikachu awakens, and his body is taken over by the orb again. He goes insane again, and one of his attacks causes a small hole that’s just big enough for him to leap through. He does so and runs off.
Brock and the others, meanwhile, are searching for Ash near the Magma chopper, when they meet up with Lance. They’re happy to see each other, and Lance removes his Magma disguise completely, as it’s no longer needed. They happen to be standing outside what apparently is the hole Pikachu made, and Ash hears them from inside. Ash tells them what happened with Pikachu. They notice something behind them, and Max exclaims that there’s a giant tsunami coming! Lance tells Ash to back away from the hole, and he then sends out his Dragonite, who uses its Dragon Claw to make the hole large enough for Ash to get out.
Meanwhile, Team Rocket is still on the shore, cowering in fear at the storm. As they sit there, Team Aqua’s sub suddenly washes up on shore along with Kyogre's tsunami, nearly crushing them! Back at the helicopter, Ash is now free, so it’s time to find Pikachu. Ash thanks Lance, and they split up. Lance rides off on Dragonite to look from the air, and Ash and his friends run off in another direction.
The scene then changes to Team Aqua. Shelly is worried about Archie, and she tells the rest of the team to leave because they’re all in danger. Flying in his mini-chopper above Kyogre, Archie is basking in his power. Riding Dragonite, Lance approaches Archie and calls for him to stop. Archie responds by ordering Kyogre to attack. It fires a Hydro Pump at Lance and Dragonite, which Dragonite is able to dodge. Lance calls for his nearby Red Gyarados to use Hyper Beam, and Archie tells Kyogre to do the same. The beams collide, and it ends in a stalemate. Archie just laughs, proclaiming that the world is his now. Suddenly, the Red Orb he’s holding absorbs into his hand, in the same way the Blue Orb did with Pikachu! Archie screams, then laughs insanely as the orb’s throbbing markings appear on his chest.
Back on land, Team Rocket discuss their situation and examine Team Aqua’s sub. When they confirm through an on board computer that Groudon is in the large metal box at the top, Meowth launches into a storybook-style fantasy about what they’d do with Groudon and Kyogre. Suddenly, a lightning bolt out of nowhere shocks Team Rocket — it’s the possessed Pikachu! Jessie comments on how strange he looks. Ash and his friends run towards Pikachu, but he leaps off the ledge he was on and lands on top of the metal box containing Groudon. Maxie and Tabitha arrive at the sub in time to see Pikachu channel the lightning from the storm into himself and amplify his power. James whips out a bazooka and aims it at Pikachu, but he quickly shocks them and sends them blasting off. Pikachu is still calling on the lightning, and everyone else can do nothing but watch. Then, the biggest lightning bolt yet comes crashing down towards Pikachu and the box, sending enough of a shock through the containment system to awaken Groudon! Archie and Kyogre watch intently as the lightning creates an explosion and Ash screams out for Pikachu. The volcano on the island erupts as Groudon’s Drought Ability begins to take effect, bringing an end to the storm. Groudon then comes into full view, and Pikachu lands on his head. Ash and his friends are happy that he’s still alive. Kyogre roars and launches a yet another tsunami, which even bigger than the last one. Groudon has things under control though, as it powers up and launches a Solar Beam at the giant wave, causing it to evaporate. On land, members of both teams comment on how truly powerful Groudon and Kyogre are. Apparently, neither side had realized it would come to this. Still on Dragonite, Lance notices Pikachu on Groudon’s head, and lands next to Ash & co. Lance warns them of the danger and says they should make a run for it. Ash says he won’t leave Pikachu, and his friends agree to stay as well. They also decide that since Pikachu has apparently sided with Groudon, they will too.
Out on the water, Kyogre fires a Hydro Pump at Groudon, and Max exclaims that the attack would do major damage because of Groudon’s Ground-type. Groudon is safe though, as Pikachu deflects the attack with a super-powered Thunderbolt. The sun’s rays are beginning to energize Groudon now. Lance tells Ash to come with him, and tells Brock and the others to take his Red Gyarados and try to stop Archie. Just as Dragonite carries Ash and Lance out over the water, Kyogre pulls Groudon underwater. Ash screams out for Pikachu, but Lance says to wait. Sure enough, they both resurface. As Kyogre’s Hyper Beam collides with Groudon’s Mud Shot, Brock and May go into action, sending out Mudkip and Beautifly. Their Pokémon attack Archie’s mini-chopper with Water Gun and Silver Wind respectively, causing it to momentarily go out of balance. Archie notices their presence, and he sends Kyogre after them. Max calls for Gyarados to swim away. As they keep Kyogre occupied, Groudon fires a Solar Beam at it. Archie alerts Kyogre, who puts up another giant wave as a shield, but the Solar Beam bursts right through and scores a powerful hit on Kyogre, sending it flying back to land in the water again. Above, we see Archie’s body rejecting the orb, which was apparently caused when Kyogre got hit. The orb emerges from Archie’s body, and Archie faints and falls off his chopper, but Dragonite catches him. The same thing that happened to Archie is also now happening to Pikachu. He yells as the orb removes itself from his body. Pikachu faints as well and falls off Groudon’s head, landing in the water. Ash promptly leaps off Dragonite, diving in after Pikachu. Brock tells Gyarados to go down and save them. Ash catches Pikachu underwater, but Kyogre is approaching them!
The scene then changes to the shore. Lance and Dragonite have landed with Archie. Lance, Dragonite, Tabitha, and Maxie look on as Shelly worriedly tries to get Archie to wake up. He slowly comes around, but seems to have no memory of what happened while he was possessed by the orb.
Presently, Ash and Pikachu emerge from the water, on Kyogre’s back! Gyarados catches up to them, and Ash’s friends ask if he’s all right. Ash tells them that Kyogre had saved him, and then Pikachu wakes up. Ash and Pikachu have a happy reunion. Lance and Dragonite show up next to Ash, and Lance asks if he’d like a ride back to shore. Max then points out the two orbs, rising in the air and circling each other. They combine into one, and then dissipate. Groudon and Kyogre stare at each other briefly, and now that neither of them is linked to an orb, they retreat back to their respective lairs: Groudon into the volcano, and Kyogre to an ocean trench. Lance and the others discuss the day’s events, and Lance says that the two legendary Pokémon will start a new world, as Ash wonders where they’ll go.