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, Patrick and Sandy get to Neptune's Paradise, but an employee tells them that the park is closed to make way for a private party, upsetting SpongeBob and Patrick and causing them to cry (although Patrick was only wailing and banging his arms and legs on the floor as if he was having a tantrum). He says it is "SpringBoob SquirePin's" party, but Sandy corrects him. SpongeBob and Patrick are overjoyed, and several characters that they met throughout the game jump out yelling "Surprise!". They all have a good time.
The ending shows them all leaving Neptune's Paradise, except Patrick, who is still in the bumper boats.
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."
In chapter one when Mr. Krabs is naked in the Barg'N-Mart, a pile of cans in the foreground are covering his crotch. When pointing the cursor over them, the game will say "Look at Strategically Placed Cans."
When pointing the cursor over the giant candle in the room with the Slot machine in chapter two, the game will say, "Look at Giant Freakin' Candle."