Ash is ready to board the ferry to Ever Grande City when May comes running up—she's won four plane tickets to Ever Grande! Except once the kids are onboard, the flight crew turns out to be Team Rocket in disguise, and the plane is headed for Team Rocket headquarters! Now if only Team Rocket had thought to fill up the fuel tank first...
Out of fuel, the plane makes an emergency landing on an island in the middle of the ocean. As Ash and his friends exit the plane, they meet Robin, a traveling salesman who's been stranded on the island for ages. Luckily, he also made a Wailmer friend to help him out! But Wailmer wasn't strong enough to carry Robin past the whirlpools that surround Wailmer Island, as Robin now calls it. Team Rocket tries to swim for it themselves, and find out firsthand how dangerous the whirlpools are!
Brock realizes that with help from their Pokémon, the group can convert the airplane to a ship. Once the ship is finished, Team Rocket grabs Pikachu and steals the ship, but once again they've forgotten about the need for fuel. The ship ends up wrecked in a whirlpool, and Wailmer helps Ash save Pikachu just in time.
Together, Wailmer and Pikachu stop Team Rocket, and Wailmer evolves into a huge Wailord! Now Wailord is strong enough to carry Robin, Ash, and his friends through the whirlpools and safely back to the ferry. But Robin, who realizes he never truly enjoyed his job in the city, decides to return to Wailmer Island with Wailord and live life to the fullest. As he departs, Ash and company turn their sights towards Ever Grande and the Hoenn League competition two weeks away!
Ash and his friends are looking for a quick escape to Ever Grande City, but May is nowhere to be found. Max suspects that she has gone to shop. But May comes back to them telling that she has won airplane tickets to Ever Grande City. Ash thinks that it is a great idea because a quick trip would give him lots of time to practice before the Ever Grande Conference begins. While the group enjoys their chartered flight, the air hostess, Jessie in disguise, announces that they will be taking a detour to Team Rocket HQ. Ash is confused at first, though realizes they have been caught in another Team Rocket scheme when Jessie removes her disguise and reveals that Meowth and James are piloting the plane. However, since the Team Rocket trio did not plan ahead, Jessie did not refuel the plane. All of them think that they will crash. However, James spots an island in the sea. Meowth, with extreme difficulty, lands the aircraft on the island.
On the island, they meet a gentleman named Robin who has been stuck on the island for quite some time. He provides everyone with some food while he explains how he came to be on the island, which he calls Wailmer Island. Following a storm, everyone was forced to abandon ship, though Robin fell into the ocean during the evacuation effort. A Wailmer saved him from drowning and brought him to the island, and the pair have since become friends. Robin tells them that all his attempts to escape from the island have failed; they might have to live on this island forever. Brock comes up with a plan to pass through the whirlpools - use the aircraft to make a boat. Thus, with a team of Pokémon at hand, the team starts building the boat. Team Rocket also helps, all the while conspiring to run away with the boat and Ash's Pikachu.
The next day, when everybody wakes up, they are startled to find that Robin had woken up before any of them. He tells that he is saying a final goodbye to Wailmer. He reflects on his time on Wailmer Island, admitting that when he was a traveling salesman he was a busy, robotic-style worker. But after he came to the island, due to his friendship with Wailmer, he began to understand the real meaning of life. Just then, Team Rocket capture Pikachu with one of their extendable arms. They also take the boat and then try to run away from the island, but are stuck as there's no fuel. Thus they are sucked in by one of the whirlpools, destroying the vessel in the process. Yet again Wailmer comes to the rescue of Team Rocket. However Team Rocket try to take Wailmer and cross the whirlpools. But, just about that moment, Wailmer evolves into a Wailord. Wailord glows again. This time, it uses Water Spout on Team Rocket and sends them blasting off.
Robin, Ash and company decide to use Wailord to cross the whirlpools. Wailord does this with extreme difficulty, but crosses the whirlpools with a jump and Water Pulse on an incoming tidal wave. The group along with Robin and Wailord find a passing ship and board it. Robin, however, chooses to return to Wailmer Island to live with Wailord and avoid his dreaded city lifestyle, as he feels that the island has given him the real meaning of life. Ash and the others are surprised, but respect Robin's wishes. Thus he sails away to the island while the group continues toward Ever Grande City.