The GBA version of Revenge of the Flying Dutchman is still a typical platforming game. There are 5 worlds in the game: SpongeBob's Home, Jellyfish Fields, Krusty Krab, Tea at the Treedome Tea at the Treedome, Doubloon Bonus World, and a final world on the Flying Dutchman's ship. Needless to say, it differs dramatically from the console versions, and the plot changes. It starts off with SpongeBob giving Gary the Snail a walk through Jellyfish Fields, Gary then smells Kelp nip and runs off. After SpongeBob finds Gary with the help of Patrick Star, he finds a chest. Gary opens it, and SpongeBob finds a big sack of coins and the Flying Dutchman boss appears. After The Flying Dutchman is defeated, the player is given a list of wishes to choose from, one of them involving giving SpongeBob his own TV show. When chosen, a screenshot of the show's original logo appears. Then you can replay all the levels and play as SpongeBob, Mr. Krabs, Gary, Sandy, Squidward, Patrick, and/or Plankton.
Source: Wikipedia, "SpongeBob SquarePants: Revenge of the Flying Dutchman", available under the CC-BY-SA License.