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've cost a fortune; however, they were free.
SpongeBob and Patrick get on the bus but suddenly, the weather gets really bad, so they get lost and end up stuck in Rock Bottom (again). The bus driver refuses to drive out of Rock Bottom until the storm passes, so the goal is to figure out why the weather is stormy and to try and fix it.
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 (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, (a green baseball cap, a lavender shirt, a camera, and his usual green swim trunks with purple flowers), was first seen on him at 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, "Ooo! 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 SpongeBob game to be released, and in Europe, SuperSponge also came out before-hand. However, Operation Krabby Patty was the first SpongeBob 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."
When Mr. Krabs opens the envelope containing tickets to Neptune's Paradise, the name "Nickelodeon" can be identified on the blurred-out stamp.
SpongeBob has a pinup of Sandy in his locker at the Krusty Krab.
When the rocket in Sandy's treedome is blasting off at the end of Chapter 3, there are two trees in the treedome. This is likely an error in scene production.
After talking to the information lady in Rock Bottom, she says, "You can check out any time you like - but you can never leave." This is a reference to the song "Hotel California" by The Eagles.
The names of the two characters, Marty and Nelson, might be a reference to the actor and musician named Marty Nelson.
How SpongeBob cries in the ending after finding out that Neptune's Paradise is closed is a reference to the episode "Pizza Delivery.”
In the "Rock Bottom" level, all of the characters talk normally, while in the show they make a noise with their tongue after every word. This shows us that everyone except Marlin just works there and is not native to Rock Bottom.
Grandma SquarePants is listed as Grandma Sponge in the manual.txt file and the credits for this video game.