When Barlow is reported missing in Boyleland, the player is sent to find him. Traveling to the back of Volcano Cave, he/she discovers a hidden harbor where the Cargo Ship is docked and witnesses Barlow being carried onto it as a hostage. Sneaking past the guards, the player boards the ship in order to rescue him.
Upon reaching the deck, Mr. Kincaid comes out of the bridge and introduces himself as Kincaid, underboss of Team Dim Sun. He brings out his Drapion and Barlow challenges him, while the player must battle several Team Dim Sun grunts who all jump overboard upon defeat. The Team Dim Sun grunts send numerous Pokémon, including many Rhyhorn. Kincaid's Drapion breaks Barlow's styler, so the player must capture it. Once Kincaid is defeated, he orders a massive valve called the Kingston Valve to be pulled so the ship will sink. He then leaves riding his Gliscor. The player goes to put the valve back in place as Barlow crash-lands the ship at the Ranger school port, saving all the Pokémon of Boyleland.
It is possible to die here if time runs out. When the in-game timer reaches a certain time, the ship will shake, the screen fades to black and says the ship was pulled under the waves. This marks the first and only time a player can die in the Pokémon games.