Unsere Freunde treiben auf Baumstämmen auf offener See, als plötzlich ein rotes Unterseeboot vor ihnen erscheint. Es gehört Team Magma. Maxie, der Führer von Team Magma erzählt ihnen, dass er den blauen Ball in seinem Besitz hat, der ihm erlaubt, Groudon zu kontrollieren. Leider hätten sie aber gegenwärtig das Ur-Pokémon Kyogre in ihrem Besitz.
After being blasted into the sea at the end of the last episode, Ash and co. are still drifting, with the boat that was to take them to Mossdeep long gone and no land in sight. The gang are overjoyed when a sub rises nearby, but once after sneaking aboard their joy turns to fear when they realise that the sub belongs to Team Magma which is on their main HQ and despite trying to hide, the gang are spotted by Team Magma's leader, Maxie. Under arrest, Maxie tells the group about Team Magma's ambition to increase the amount of land on Earth by awaking the legendary Pokemon Groudon, and in order to help with this Team Magma have already captured Groudon's nemesis Kyogre as well as the Blue Orb that controls it, which they plan to swap with Team Aqua for the Red Orb. Meanwhile, Tactical Commander Shelly of Team Aqua is also aboard the base and sets about releasing Kyogre, but when the huge Pokemon gets free it begins to tear up the place, causing the Blue Orb to fuse with Pikachu making it super-powered. While Ash and Pikachu are separated from Brock, May and Max, Lance arrives to help with the situation but things get worse when Archie and Team Aqua turn up...
Sin querer queriendo, los chicos se encuentran con el Equipo Magma que está planeando cómo obtener a Groudon de las manos del Equipo Aqua, mientras tienen a Kyogre en las suyas.
トクサネシティへむかって船で旅をつづけるとちゅう、ロケット団にピカチュウをうばわれそうになったサトシたち。その戦いのさいちゅう、ピカチュウの電撃（でんげき）がひきおこしたばくはつで、サトシたちとロケット団は海にとばされてしまった。そこへとつぜんあらわれたマグマ団の潜水艦（せんすいかん）は、サトシたちをつかまえてしまう。
「超古代（ちょうこだい）ポケモン」グラードンの力をりようして世界せいふくをねらうマグマ団は、ついにカイオーガをはっけんしていたのだが…。
Vore helte er blev reddet i åbent hav og befinder sig nu om bord på Team Magmas undervandsbåd. Her får de et større indblik i bandens planer om verdensherredømmet!
