Ash and his friends are on the boat deck discussing their expectations for their adventures in the Whirl Islands. Their ferry soon approaches several large whirlpools, instantly alarming the group. However, two attendants, who are actually Jessie and James in disguise, on the ferry offer them drinks and assure them that it's all right, as they pass through the sea of whirlpools harmlessly. James prepares to net Pikachu, but some turbulence leads him to instead catch Ash. Ash frees himself easily and asks for answers, and Team Rocket promptly reveal themselves. Jessie and James call on Arbok and Weezing to use Poison Sting and Smog, respectively. Ash tries to end the squabble quickly and orders Pikachu to use a Thunderbolt. However, Jessie has Wobbuffet Counter the attack, thereby causing a massive surge that sends Ash’s group and the Rocket trio overboard.
Ash and his friends panic as the ship continues ahead and they are soon being sucked into a whirlpool. Misty calls out Goldeen and Poliwhirl, while Ash gets out Totodile. They start to swim away from the whirlpool, but soon they get dragged in again. The currents suddenly change, and the group realize they are safe. They watch as a mysterious silhouette swims underneath them and hear a peculiar call. A Pokémon comes after them shortly, and Brock realizes it's a Corsola. The Corsola races towards them and circles around them. Soon they are picked up by some tentacles, which they realize is a Tentacruel, and soon taken towards a boat. Misty is enjoying herself, but the others seem quite afraid. The Corsola leaps from the ocean and into the arms of its Trainer, Professor Elm, who happens to be on board.
Professor Elm and Ash spend some time catching up, and Misty admires the Professor's Corsola. He takes a few minutes to explain to Misty about Corsola and its abilities. Elm is thrilled the kids are safe because of Corsola and Tentacruel's efforts. Captain Marius enters the room and introduces himself. Soon Marius drives his ship to Blue Point Isle's Inland City, the entry way to the Whirl Islands. The group notice the city is particularly colorful, and Marius and Elm informs them that it is all for the upcoming Whirl Cup, a Water battle tournament held every three years. Misty is instantly keen to compete, and Professor Elm explains that the event is more than a month away. Meanwhile, Team Rocket has washed ashore and they decide that lunch is in order before they hatch their next grand scheme.
The group decide to go to the Pokémon Center where Nurse Joy hands Ash an official Whirl Cup guidebook and registers both Ash and Misty for the competition. Marius notices that Brock hasn't registered yet, but Brock explains that he is more interested in understanding Pokémon. While Corsola plays in the Center pool, Professor Elm informs Ash and Misty that many Whirl Island Trainers specialize in Water Pokémon. Ash feels a little uneasy about the tough competition, though Misty feels right in her element. Elm shows the pair a map of the Whirl Islands and says that the Whirl Cup will be held on Red Rock Isle, two islands north of their current location. Meanwhile, Team listens in from behind some bushes and set their sights on stealing the powerful Water Pokémon for themselves.
Later, Marius and Elm are busy preparing a submersible machine for their next expedition. Ash and his friends approach them about the mysterious creature they saw earlier. Captain Marius is unsurprised and hints that local legends of such a creature do exist. Elm admits that the world of Pokémon is full of mysteries and explains that the Steel-type classification was only added in recent years. Elm admits that these mysteries have motivated his research and clarifies that he is currently investigating the ocean because it thought to be the origin of all life. Marius suggests the kids should follow their dreams, but enjoy the ride as well.
On the boat, Elm notices a balloon heading towards them. The group instantly recognize it as Team Rocket's trademark Meowth balloon. The balloon drifts towards the Pokémon Center where it releases a net and swipes all the Pokémon in the pool. Team Rocket are pleased with their easy catch, but the celebration is interrupted when Marius pursues them with his boat. Jessie calls out Arbok, which swims towards the vessel. Ash tells Pikachu to go after Arbok, but Misty stops him. Instead, Misty releases Staryu to battle Team Rocket. Staryu starts off with a Swift attack, and it hits Arbok. Staryu uses Water Gun, but this time Arbok dodges and counters with its Poison Sting attack. Misty is forced to recall Staryu, but before she can release another Pokémon from her team, Psyduck comes out. Psyduck bravely jumps into battle, but has trouble swimming and Misty returns it to its Poké Ball. Ash finally gets a chance to fight and Pikachu attempts a Thunderbolt, but James gets out a net launcher and fires it, snagging Pikachu. With Misty and Ash both defeated, Corsola jumps into the water. Elm tells it to do a Tackle attack, however, James has Weezing strike back with a Sludge attack. Corsola manages to dodge all the Sludge and Tackles Arbok, sending it flying into Weezing and directly into the Rocket's balloon basket. Following instructions, Corsola fires Spike Cannon at the Meowth balloon, cutting up the nets and the balloon, sending Team Rocket blasting off and freeing the stolen Pokémon. Elm is surprised by Corsola’s performance and jokes that he will stay on its good side.
Overnight, Ash contacts Professor Oak on the Center's videophone to discuss the mysterious Pokémon he saw. Though Elm soon takes over the conversation to talk about theories with his mentor. The following day, Marius tells the group they should take the next ferry from Bluefinland to reach Yellow Rock Isle, and Brock confirms the details in his handbook. The group soon heads on foot towards Bluefinland and they wave goodbye to Professor Elm and Captain Marius.