After winning his Gym battle against Roxanne, Ash is psyched and ready for his next Gym battle on Dewford Island. As he and his friends walk towards the port to catch the ferry, May suggests that they get some of Rustboro City's famous pasta. She has directions to the restaurant that she printed off the internet, but when they arrive they find the restaurant empty and boarded up. She realizes that she forgot to check the date on the map and it's ten years old. Everyone is starving and not too happy, and to make matters worse, since the directions were written the port has been moved to the other side of the bay.
Since they've already missed the ferry, they decide to relax until the next one comes, though Ash is depressed because he wanted to have his Gym Battle right away. May decides to try to find a boat, figuring that since it used to be a port, there must be a boat left somewhere. She doesn't have any luck and she doesn't even see any people either, until she spots an old man fishing off the pier. At first, he thinks that she wants to know why the fish aren't biting, and then realizes he doesn't even know who she is. Just then, a Wingull flies down and the old man greets it, calling it Peeko. May thinks it's cute and tries to make friends with it, but it hides and the man tells her that the only person it likes is him. However, it warms up to her and she gives it some Pokémon food. The man introduces himself as Mr. Briney. He tells May that he's the only one left in the old port who still has a boat, and he happily offers to take her and her friends to Dewford Island. He says that when he was young, he was a great sailor, though his seafaring lingo leaves May confused. Team Rocket overhears the entire conversation as they wait from behind a rock. Jessie sets her sight on Peeko, because it's almost as cute as her "Little Wurmple-y Poo." After May has left to get her friends, someone in a blue bandana is spying on Mr. Briney.
May guides Ash, Brock, and Max over to Mr. Briney's place. They're glad that she found a boat, but unsure about how trustworthy Mr. Briney is. May assures them that he used to be an amazing sailor, butchering the pirate talk that he used before, but they are still unconvinced. But when they arrive at his house, he screams at them that he never met May before and he won't take them in his boat before slamming the door in their faces. The others are rather suspicious about whether May was telling the truth, and they all walk away sadly. Mr. Briney peers through his window for a moment before drawing the curtain shut. He says that he didn't want to put those kids in any danger, as the man who was spying on him stands behind him. Mr. Briney knows that the man is from Team Aqua. The grunt wants the boat, and Mr. Briney has no choice since the man's Crawdaunt has Peeko in a cage.
May is upset because she doesn't understand why Mr. Briney treated her that way. They have no choice but to walk to the other port and try to catch the afternoon ferry. Suddenly, Officer Jenny pulls up on her motorcycle and she quickly recognizes the group from yesterday. She warns them that the area is dangerous; the man from Team Aqua they met at the Devon Corporation the day before is somewhere in the area, and other members are planning to meet him. Max and Brock use their deductive reasoning skills and figure out that since there are checkpoints on all roads out of the city, the Team Aqua members' best way to escape would be the sea from the old port. Mr. Briney has the only boat in the whole port, so they realize that he might be in trouble.
The Team Aqua grunt and Mr. Briney are preparing to board the boat when they hear people calling Mr. Briney's name. Ash and friends are banging on the door, but then Max notices the dock around the back of the house. The Team Aqua grunt sends Crawdaunt to block their way, and the group notices that it is holding Peeko in a cage. Pikachu and Crawdaunt charge forward, only to be stopped by a rain of smoke bombs – it’s Team Rocket. They recite their motto and use a giant vacuum to suck up Pikachu and Peeko. Brock has his Lotad use Water Gun on the balloon, breaking the controls of the vacuum and releasing Peeko and Pikachu. Mr. Briney runs to retrieve Peeko, but Crawdaunt gets to it first. A Bubble Beam from Crawdaunt sends Team Rocket blasting off. The grunt takes the opportunity to jump in Mr. Briney's boat, along with Crawdaunt and Peeko, and takes off. He's no doubt going to meet up with the others, but without a boat, Ash and his friends can't catch him. Luckily, they have a boat. Mr. Briney pulls a lever in his boat storage room, and all the water drains away, revealing a high tech boat, the S.S. Wingull. They speed off to follow the grunt, Mr. Briney remembering how after he retired he was bored until he became inspired to sail again after meeting Peeko, so he built the Wingull boat.
The grunt is headed toward the rendezvous point, and he speeds up after seeing the S.S. Wingull closing in. They realize that he's going to meet up with the other Team Aqua members at Triangle Rock up ahead, so Ash and Pikachu go on deck to try to stop him. Crawdaunt strikes first with a Water Pulse and sends the boat flying. It follows up with Bubble Beam on the ocean surface, causing a huge wave to wash over the S.S. Wingull. Though Mr. Briney's vessel doesn't suffer any damage, the grunt is almost to Triangle Rock and he's going so fast, he's going to crash into it. Ash has Pikachu use Thunder to destroy the rock, but a lot of it still remains. Mr. Briney makes a sharp turn and cuts in front of the other boat, angling his vessel so that it serves as a ramp and the other boat is launched over the rock. He jumps into the water and swims out and grabs Peeko. Just then, a massive Team Aqua submarine surfaces and the grunt they were chasing goes inside. As the submarine submerges again, Ash wonders who Team Aqua is. That night, back at Mr. Briney's house, Ash and friends realize they haven't eaten since breakfast. May is still sad about the pasta, but it turns out that the pasta restaurant was owned by Mr. Briney's best friend, so he calls him up and asks him to make them some of his pasta for dinner. The next day, they all board the S.S. Wingull and set out for Dewford Island.