After being freed by SpongeBob, Triton captures King Neptune and everyone else at the Krusty Krab, and SpongeBob and Patrick try to sneak into the Krusty Krab to free everyone. Triton then transforms Bikini Bottom into Mount Triton and turns all the Krabby Patties into monsters while sending SpongeBob and Patrick down the mountain.

During their failed mission they find the tridents of King Neptune and Queen Amphitrite, which gives SpongeBob and Patrick new powers, such as super strength. The two then start climbing the mountain, fighting their way to the summit in hopes of rescuing the captives and defeating Triton.

As SpongeBob or Patrick, the player has to travel to the summit of Mount Triton while cleaning up Bikini Bottom. To do this, they must go through each level and use their powers to destroy every contaminated building in the level, which causes a clean version of the building to spring up in its place. The player can climb up buildings and hop from one building to the next in order to help them succeed. There is also a time limit on how long the player can take to complete the level.

While SpongeBob and Patrick do this, various Krabby Patty-themed enemies will spawn with the intent on damaging the player. While many of these enemies are basic grunts, some have special abilities, like piloting a helicopter that shoots coconuts. The player can eat some of the basic enemies to regain health and other effects. If the player runs out of health, they lose.

During SpongeBob and Patrick's journey, they will earn Smiting Points, earned by filling a meter through attacking buildings and enemies. Smiting Points are used to upgrade the player's jump height, speed, health, and ultra move. An ultra move can be performed by charging up the attack button, and releasing it when at least one of the three circles at the top-right corner of the screen is filled.