The game is done in the style of tower defense with the main objective being to defend the Krusty Krab from Plankton's army of robotic clones. With an array of weapons, the player has to use their limited supply of currency to strategize an effective plan to save the clones from entering the Krusty Krab.
Funnily enough, there also exists a level title in Operation Krabby Patty called Invasion of the Patty Snatchers.
There is a glitch in the game that allows the player to get an infinite amount of money. To do it, the player must place a tower, select it, pause the game by clicking "Menu", and then click "Sell". The tower will be "sold" and will give you the money, but will not disappear. You can continue clicking "sell" to get more money from the same tower. Using the same glitch, you can instead click "upgrade", and assuming you have the funds for it, you can infinitely upgrade the tower and give it the maximum damage and range possible.