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...
A young boy named Ash Ketchum embarks on a journey to become a "Pokemon Master" with his first Pokemon, Pikachu. Joining him on his travels are Brock, a girl-obsessed Rock Pokemon Trainer, and Misty, a tomboyish Water Pokemon Trainer who may have a crush on him. Ash and Co. end up traveling through various regions, including Kanto, the Orange Islands, and Johto, and then enter the Pokemon League competitions there.
Along the way, they run into many confrontations with Jessie, James, and Meowth, a trio of Pokemon thieves who are apart of an evil organization called "Team Rocket". But every time Team Rocket try to do their evil deeds, they fail thanks to Ash and his Pokemon.