SpongeBob wins the "Employee of the Month" award once again, so Mr. Krabs decides to name him the "Employee of the Year." He then receives a mysterious mail package containing two free tickets to "Neptune's Pacific Paradise," and later gives them to SpongeBob for winning the "Employee of the Year" award, with SpongeBob saying they must of cost a fortune; however, they were actually free.
They get out of Rock Bottom, but SpongeBob and Patrick do some annoying things on the bus, so the bus driver tricks them and says that the bus ran out of gas. They get left behind and have to find a new way to get to Neptune's Paradise. The goal is to get on Sandy's rocket.
The oxygen fuel tank in Sandy's rocket runs out of oxygen fuel (thanks to Patrick stepping on the gas pump), and they get stuck in Bottoms Up. The goal is to get the oxygen tanks filled at a place called Oxygen Springs so that SpongeBob and Patrick can get to Neptune's Paradise. But the real question is "where will Spongebob find a jacket?"
In the ending sequence, SpongeBob and his friends get to Neptune's Paradise, but an employee tells them that the park is closed to make way for a private party, breaking SpongeBob and Patrick's hearts. SpongeBob and Patrick cry (although he was only yelling and banging his arms/legs on the floor as if he was having a tantrum). He says it is "SpringBoob SquirePin's" party, and Sandy tells him that he made an error in pronunciation. SpongeBob and Patrick are overjoyed as their hearts are fixed, and several characters that they met throughout the game jump out and say: "Surprise!" They all ride the rides and have a lot of fun.
The ending shows them all leaving Neptune's Paradise, except Patrick, who is still on a ride.
The outfit that Patrick wears throughout most of the game, (consisting of a green baseball cap, a lavender shirt, his usual green swim trunks with purple flowers, and a camera), is seen on him in the beginning of "Neptune's Spatula."
If the player clicks on the Operation Krabby Patty poster inside WSEA TV, SpongeBob breaks the fourth wall by saying, "Ooooh, Operation Krabby Patty, that was my very first game. Good times, good times."
Technically, this is not true because Legend of the Lost Spatula was the first official game to feature SpongeBob SquarePants. However, Operation Krabby Patty was the first PC game.
In Chapter Two, there is a man named Jojo fixing an antenna who asks SpongeBob for a soda and SpongeBob gets him a Diet Caffeine Free Coral Cola with a Lemon Twist; the drink is a reference to the episode "No Weenies Allowed."