The player's objective is to save Gary from the Flying Dutchman. After four levels, SpongeBob and Patrick fight the Dutchman and rescue Gary. However, after they do so, the Flying Dutchman will chase them with his ship and they will have to play the levels in reverse.
The player moves with the left and right arrow keys, ducks with the down arrow, and jumps with the up arrow. The spacebar uses the player's power-up.
If SpongeBob gets hit by a hazard or falls in the water, then Patrick takes over next to where SpongeBob failed at. If the same happens to Patrick then you lose a life. SpongeBob goes back to the start or the checkpoint if it was obtained. Each level has a checkpoint halfway through the level. If you lose all lives including 0 or you ran out of time then it's game over and the mission was not accomplished. If you beat all 9 levels then the mission will be accomplished and you win the game.
Bubble Buddies: You get an extra life every time you collect 100 Bubble Buddies. There are three types - purple ones are worth 1 Bubble Buddy, blue ones are worth two Bubble Buddies, and yelIow ones are worth 3 Bubble Buddies.
Clam: Jumping on clams gives you goodies! Some clams spawn a power-up when jumped on, and others give you Bubble Buddies the first five times you jump on them.
Jellyfish: This power-up allows SpongeBob and Patrick to throw electrified jellyfish that kill enemies on contact. The jellyfish bounce on the floor, and no more three of them can be onscreen at a time.
Pufferfish: This power-up allows SpongeBob and Patrick to inflate and grow spikes on their bodies for a few seconds, killing any enemy that touches them while they're inflated. If this ability is used while the character is running, he'll also slide across the ground, making it easier to destroy enemies in your way.
Hook: Each stage has one hook in it. If you manage to find one, it'll give you a free ride, allowing you to skip some of the level you're on.
Enemies and hazards
Ghost snail: This enemy moves back and forth across the ground or platform he's on. Jumping on him will only make him hide in his shell; use power-ups to kill a ghost snail.
Ghost jellyfish: This enemy randomly floats around, and can be killed just by jumping on him.
Cannonball: Seen in Levels 1, 3, and 4. Cannonballs occasionally spawn from either edge of the screen and will slowly fly across. You can get rid of a cannonball by jumping on it.
Fireball: Seen in Levels 2, 3, and 4. Fireballs rain from the sky, and nothing can destroy them.
Ghost cannonball: Seen in Level 4, and also used by the Flying Dutchman's ship. Ghost cannonballs are the same as normal cannonballs, except engulfed in ghostly green flames and totally indestructible; jumping on one of these will deal damage to you!
Ghost fireball: Only seen in Level 5. Ghost fireballs are just like normal fireballs but colored green, and they only appear when the Flying Dutchman summons them with his Ghastly Laugh. Also, they only ever rain down on the floating platforms in the room.
Water: Falling into water will result in an instant death since SpongeBob and Patrick are terrible swimmers. Level 5 also has a pool of acid which has the same function as water.
The Flying Dutchman: The final boss of the game, encountered in Level 5. The Dutchman will float around the room and attack by throwing electrified jellyfish just like the ones SpongeBob and Patrick use. He alternates between sending a group of three jellyfish rolling on the floor and tossing up four jellyfish which ricochet around the room. Sometimes, he can also let out a Ghastly Laugh that will send Ghost Fireballs raining down. To defeat the Dutchman, you have to hit his head six times, either by jumping on him or hitting him with a power-up. This is incredibly easy to do if you have a power-up because once the Dutchman recovers from being hit, he immediately becomes vulnerable to taking damage again. Keep in mind, though, that Gary is also in this level, trapped in a cage suspended above a pool of acid. The cage will slowly lower itself towards the acid and if it reaches the pool, it's game over! Luckily, there's a level you can jump on to raise the cage back up to the ceiling to buy yourself more time to fight the Dutchman.
The Flying Dutchman's Ship: Beating Level 5 will result in you saving Gary...and the Flying Dutchman becoming enraged! You will then have to play the first four levels in reverse as the Dutchman pursues you with his haunted vessel! If he catches up to you, it's an instant death! In Levels 6 and 7 the Dutchman will simply come at you in his ship, but in Level 8 he'll also throw jellyfish if he gets close to you, and in Level 9 the ship will shoot ghost cannonballs!
Uptown Bikini Bottom
Downtown Bikini Bottom
Bikini Bottom Outskirts
The Dutchman's Lair
The Ghostlands Backwards
Bikini Bottom Outskirts Backwards
Downtown Bikini Bottom Backwards
Uptown Bikini Bottom Backwards
Patrick's quote "Did you see my underwear?" from The SpongeBob SquarePants Movie is reused in this game whenever he gets touched by an enemy. His "Good morning!" is taken from Help Wanted (the line in full is "Good morning, Krusty Krew!").