Ash is admiring his two Orange Crew Badges and Tracey tells him he needs two more to enter the Orange League. Ash wonders whether it would be easy to earn them. They come across Moro Island and long for a nice meal at the Pokémon Center. After supper, they call Professor Oak, who tells them a 300 year-old official Orange League trophy has been found. They decide to go to the museum the following day just to take a look. Meanwhile, Team Rocket breaks into the museum and steals the trophy. During the escape, James accidentally falls and leaves his shape holding the trophy on the ground. When Ash and his friends get to the museum, a crowd is waiting outside. Officer Jenny is keeping the door and tells them the trophy has been stolen. A pair of footprints and the shape in the mud of the unknown thief holding the trophy are the only clues. Ash, Misty and Tracey decide to investigate. Not far from there, they find Team Rocket behind some bushes, mentioning their mischief during the previous night. Ash and friends begin chasing them, but Team Rocket escapes using a Seadra-shaped boat. The heroes get on Lapras and continue the chase. Suddenly, a thick fog catches Team Rocket, who eventually find an abandoned ship in the middle of the fog. They decide to use it as a hideaway, but a ghost appears just behind them. Scared, they try to run away, but the ship is in a poor condition and they fall through the floor to a lower level. Now two ghosts begin harassing them and take the trophy from James's bag. After that, the two ghosts attack Team Rocket and haul them off. Ash and friends find the ship and notice the Seadra-shaped boat is empty just next to it, a sign that Team Rocket is surely hiding in the ship. As they get on, Misty starts shivering and Togepi falls into a hole in the floor. The gang starts looking for Togepi all around the ship, when they finally find it, playing with the two ghosts in one of the cabins. The Orange League trophy is laying on a bedside table. Ash sends out Bulbasaur, but it stops its attack because it seemed the ghosts were playing with Togepi, not frightening it. So Misty calls for Staryu, who uncovers the true identity of the ghosts behind the sheets: Gastly and Haunter. Ash and friends say they want the trophy for the museum, but Gastly and Haunter refuse to hand it over. Team Rocket gets to the cabin and starts fighting the ghosts to get the trophy back, but they are unsuccessful and faint. Haunter takes control of Meowth and makes it relay the history of the two ghosts. Meanwhile, Captain's Haunter creates an illusion to show with images what Haunter was talking about. Three centuries before, the Gastly and Haunter's Trainer was the captain of the ship. He was a well-known Pokémon Trainer and managed to win the Orange League. The ancient trophy on the bedside table belonged to him. But a sea storm put an end to his life and the ship sank. Gastly and Haunter had watched over their master's trophy for three centuries until some weeks before, a group of researchers found the sunken ship and took the trophy away. They drove the ship to surface again to recover it, and now they had it back, they would leave with it. When Haunter finishes talking, Meowth wakes up Jessie and James and they try to fight the ghosts again. Once more, they are blasted off. Ash and friends understand the Pokémon's loyalty to their master even 300 years after and respect their decision. Ash says whether the captain was or not around there is not an excuse to take what belongs to him from where it belongs. They finally say goodbye to Gastly and Haunter, who take the ship to the sky and take it to a place where it could not be found.

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