The Flying Dutchman's ship is a large and flying pirate ship. Like the Dutchman himself, the ship has a green tint and garners a ghostly glow. The sails are rotting and moldy, and dust hangs off of the ropes. It is noted by the Dutchman that he always wants his ship to look "good and scary." Because of this, he is content when his ship is in a state of disrepair, as these touches add a certain spooky atmosphere to the vessel.
It is revealed that there is a large perfume department in the crew's quarters. The Perfume Department can serve as a viable escape route from the crew's quarters and should anyone try to attempt to brave the creatures that reside within.
Despite the non-corporal nature of the ship, it shares a few of the Dutchman's characteristics. Apart from the ship's ability to fly, the ship itself is rooted mostly in the physical world. Living beings like SpongeBob and his friends are more than capable of standing on the deck of the ship without falling through, and the ship itself has been partially or completely destroyed by terrain on several occasions.
While Mr. Krabs, SpongeBob, and Patrick are digging for the Flying Dutchman's treasure, the Flying Dutchman is seen in his bed on his ship. After being woken up by all the noise below, he interrogates the three on why they dug up his treasure.
The anchor from the ship crashes into SpongeBob and then Squidward's house. Squidward, angered, climbs up the anchor rope with SpongeBob and Patrick. They look around before trying to figure out whose ship it is. When SpongeBob and Patrick try to escape, they keep ending up back on the ship. SpongeBob and Patrick end up locked in the ship.
The ship appears when the Flying Dutchman finds Lord Poltergeist, his former first mate. When the gang tries to escape from him, he chases after them in the ship, before dropping a nuclear bomb onto them from his ship.
The ship appears over Bikini Bottom while the Flying Dutchman looks down on the town being scared on Halloween. Later, he brings the souls of SpongeBob's friends aboard to try and scare SpongeBob. SpongeBob and Patrick end up going through a horrific ride through his ship, surrounded by scary puppets.
One day, while getting ready to leave for work, SpongeBob tells Gary that he had a bad dream the previous night and the latter conveys that he had a bad dream too, so SpongeBob tells Gary that he will play fetch.
After getting the stick, SpongeBob tells Gary to fetch his "favorite fetching stick." However, Gary brings back a chest. SpongeBob opens the chest only to find a series of consecutively smaller boxes. Eventually, he discovers a bottle which he then opens and unwittingly releases the Flying Dutchman.
The Dutchman starts hypnotizing the citizens of Bikini Bottom to join his ghostly crew with an object of their desire, leaving SpongeBob to save them and defeat the Dutchman by himself.
SpongeBob is walking Gary through Jellyfish Fields, when he suddenly smells Snail Nip and runs away. SpongeBob chases after him through an empty area near his own house, encountering Patrick and Squidward along the way. This level serves as the tutorial.
After completing a path through a cave, SpongeBob finds Gary, along with a large treasure chest. He opens it, revealing a series of smaller chests and eventually a bottle, which releases the Flying Dutchman. SpongeBob mistakes him for a genie, much to the Dutchman's annoyance.
After failing to tell him of his ghostly nature, the Dutchman agrees to give SpongeBob a wish if he can find his ten hidden treasures around Bikini Bottom, along with his doubloons.
The Nicktoons reach the ship of the Flying Dutchman, a ghost that haunts Bikini Bottom.
The heroes meet him and he tells them that they can never leave. SpongeBob greets the Flying Dutchman. After realizing that SpongeBob is there, he allows SpongeBob to leave, but Danny, Jimmy, and Timmy have to stay. SpongeBob says that he cannot leave them and the Flying Dutchman will have to keep SpongeBob too. He says that he has been practicing being a pirate. The Flying Dutchman does not like the idea of keeping SpongeBob. He says that if he had his old crew back, he would not need the heroes. Danny suggests that they help get the Flying Dutchman's crew back. The Flying Dutchman says that his old crew will not listen to them. Danny says that he thinks that the crew will listen to them. The Flying Dutchman agrees and says that if the heroes can get his six crew members back, he will let them go. However, if they fail, the heroes will have to be his crew forever.
They go through several ships and get the crew back. They head back to the Flying Dutchman. He sails off. When the Flying Dutchman leaves, his anchor hits a giant door and opens it. The door leads to the Jellyfish Fortress Factory.
It is a boss fight against the Flying Dutchman
After four levels, SpongeBob and Patrick fight the Flying Dutchman on his ship and rescue Gary. However, after they rescue him, the Flying Dutchman will chase them with his ship and they will have to play the levels in reverse to get back to SpongeBob's house.
SpongeBob is trapped in the Flying Dutchman's ship and now the ship is rising to the surface and the sea water is running out. If he sees the light of day, he will dry out. The player must help SpongeBob get out of the Flying Dutchman's ship before he becomes dried up. Press the right arrow key to run right, free the left arrow key to run left. Go down thin pipe passages by running towards one and pressing down repeatedly to slide down the thin pipe passage. If the player gets caught in the fish skeletons, they have to press right and left repeatedly to get free. There are four pickups along the way placed randomly.
If the player makes SpongeBob dry up too many times and loses all the remaining lives, the player loses the game, and SpongeBob will stay in Dutchman's plate. If the player escapes though exists, SpongeBob is no longer trapped on the Flying Dutchman's ship and the player wins the game.
The Flying Dutchman has been tricked by Doodle Patrick into thinking that SpongeBob, Squidward, Patrick, and DoodlePants were his enemies. But when Doodle Patrick takes control of his ship, he realizes he has been tricked and relies on DoodlePants to stop him.
SpongeBob and Patrick have "borrowed" a chest of gold coins from the Flying Dutchman. But, the Flying Dutchman thinks they are thieves. Help SpongeBob and Patrick high-tail it off the deck. Use the arrow keys to navigate and dodge crates. Tap the space bar to jump over crates. Hold the space bar to duck under crates. The game ends when the player bumps into too many crates and lose all the gold coins.