The story mode takes place in a theater. The player is acting out a performance at the theater in front of an audience. It is a mystery game, similar to that of cases of Sherlock Holmes, and other detectives like that. SpongeBob plays the leading detective and the other characters play other parts in the game. While it seems quite simple, there is a much larger complicated system to each scene. There are three chapters overall and there are five to six scenes in each chapter. Use the mouse to direct the actors to do appropriate actions based on the instructions. The player earns stars depending on how good the performance is. Some directions are timed so they must be finished quickly or the audience will boo and the player will lose stars. Some timed directions may result in the play ending immediately if they are not completed in time. (e.g. If the player does not fling the cans at the monster, it attacks SpongeBob.) There are also clues in scenes. Those that are involved in the story will automatically be picked up, and other clues can be found hidden in scenes. Finish the play and earn as many stars and achievements as possible.
Arcade mode is a mode full of mini-games. The mini-games are small challenges that have already been completed in Story Mode.
Detective SpongeBob SquarePants is trying to stop the cat bandits, find out why monsters have been attacking New Kelp City and find the stolen Golden can of Snail-Po, all while trying to find Sandy's cat Larry. After the end of the three cases, SpongeBob figures out that all the cases are connected to each other and deduces the criminal mastermind behind all the crimes.
Chapter 1: Who's Laughing Meow?
Detective SpongeBob SquarePants is in his office and Sandy comes in with a baby (played by Patrick) telling SpongeBob her cat Larry (later revealed to be played by Gary) is missing. SpongeBob tells her that he will not help her and his hat phone starts ringing. SpongeBob answers and tells Sandy that a gang of bandits were spotted downtown. Sandy asks SpongeBob if he will help her find her cat and SpongeBob says he will not help her once more, leaving her frustrated. SpongeBob then says he has to "escar-go", and heads downtown.
SpongeBob appears outside Squidward's house and Officer Puff (played by Mrs. Puff) asks SpongeBob who invited him there. SpongeBob asks her about the gang of bandits and she (accidentally) reveals that they are cat bandits. SpongeBob asks her more about them and she refuses to tell him, but gives him clues. After deducing the snail she is giving clues about, it appears and SpongeBob wonders what Officer Puff is talking about. Officer Puff tells SpongeBob that it is her cat, Precious. SpongeBob realizes Officer Puff had the wrong idea and asks her about the gang of bandits. Officer Puff shows him a photo of the bandits (which had Larry in it) and SpongeBob says the plot congeals and asks her where they went. Patrick shows up and asks SpongeBob what congeal means. SpongeBob looks for clues and finds a trail of snail slime leading up the nose of Squidward's house. SpongeBob says he learnt how to build a ladder during his stint at Bikini Bottom prison (causing a photo flashback to appear where SpongeBob is in prison uniform humorously failing to lift weights with stuffed animals attached to them) and proceeds to build a ladder. He then climbs up into the nose of Squidward's house.
After climbing up the nose SpongeBob finds a squeak-easy where a woman (Played by Squidward) is playing the clarinet. The bartender (Played by Larry) says that he only serves cats. SpongeBob meows, but the bartender is not fooled. SpongeBob finds some cat ears and puts them on, disguising himself as a cat. SpongeBob said he was looking for someone. The bartender made sure SpongeBob was from the gang of bandits by asking him to do the "secret wiggle". After SpongeBob successfully does so, the bartender tells him everyone is at Kelp Forest Camp and SpongeBob distracts the bandits at the bar by making the lamp fall, destroying everything. SpongeBob heads towards Kelp Forest Camp.
SpongeBob arrives at the gate to the camp, but the guard (Played by Plankton) says he needs the password (Which came in the form of answering a knock-knock joke with answers related to the animal he was talking about). After giving the guard three passwords, he gets tired and lets SpongeBob in.
SpongeBob arrives at the camp and whispers to Larry that he is here to save him. Larry tells SpongeBob that he wants the golden flower that the leader of the bandits (Played by Mr. Krabs) is holding and when SpongeBob asks why, he says it is "for his mom". SpongeBob sneaks over to the leader of the cat bandits, who asks him who dares to stand before him. SpongeBob says that it is him and flips his hat back, knocking off his cat ears and revealing that he is a detective. SpongeBob tries to arrest the leader for "Catnapping", but he orders his bandits to fight SpongeBob. After knocking down a cage which crushes the leader, SpongeBob takes Larry back to Sandy with the golden flower, but Larry eats the flower first. SpongeBob facepalms himself realizing that Larry only wanted to eat the flower and takes him back to Sandy.
Back at SpongeBob's office, Sandy thanks him and asks how she can repay him. SpongeBob says that it's all in a day's work and Sandy and Larry leave the office.
Chapter 2: Keep Calm and Monster Mash
SpongeBob's office is dirty (Because of the latest CATastrophe) and SpongeBob cleans up his office. Patrick arrives with a cardboard television on his head (Acting as the news anchor) and the news is on. The news implies that there are monsters at New Kelp City. However, the television has low signal and everything on the screen is blurry. After SpongeBob adjusts the antennae and slider, Patrick humorously tells SpongeBob he is on TV, which was not supposed to happen as it breaks the play's fourth wall. Realizing his mistake, he warns everyone about the monsters again and says that New Kelp City will be saved by SpongeBob. SpongeBob says that "You can't spell "Solution" without S-P-O-N-G-E-B-O-B" and goes to New Kelp City.
SpongeBob arrives at New Kelp City. He tries to ask locals about the monsters but they interrupt him saying they want to meet the monsters. The locals call the monsters "Tourists", "Visitors" and "Newcomers". SpongeBob wonders if they are talking about the monsters so he stacks objects together and climbs up to get a better view. It is shown that a monster is eating Old Man Jenkins. SpongeBob is amazed that the locals are completely unaware of the danger of the monsters, and tries to save the citizens from the monster by crossing with a hotdog stand. After he rescues the citizens Patrick appears saying he's wearing pants and directs attention back to SpongeBob, whom he calls "ugly." SpongeBob notices a piece of paper and picks it up, revealing it is actually an flyer for a restaurant called Chewy Louie's, who owns the hotdog stand SpongeBob was driving, covered in snail slime. SpongeBob finds the flyer suspicious and visits Chewy Louie's.
At Chewy Louie's, SpongeBob looks around but nobody is around. He asks if there's anybody there, but a monster pops up from a hidden door. SpongeBob takes cover and repeatedly throws food cans at it, driving it away. After the monster goes back through the hidden door, a tile falls out, revealing a control panel to open the door. SpongeBob looks around for clues and finds a code that unlocks the door. SpongeBob opens the hidden door and goes into the room.
In the room SpongeBob tries to look around, but the lights are out. SpongeBob finds the control panel and connects the wires, turning the lights on. SpongeBob notices suspicious things like suits and shoes that resemble monsters. A monster suddenly starts talking to SpongeBob and he asks him to show himself. The monster does not show himself, but sends an floating armored monster to attack SpongeBob. SpongeBob breaks its armor and throws trash at it until it falls. The real monster then appears hanging upside-down tied to a rope by its legs. SpongeBob tells the monster that his reign of terror should end after the incident. SpongeBob tells the monster to "hang around" and that some "friends" (the police) would like to see him.
The monster is in the police van with SpongeBob ready to unmask him. SpongeBob removes the monster's mask and reveals a shocking plot twist that the monster was Sandy, who says that SpongeBob hasn't seen the last of her. SpongeBob feels that it makes no sense that it was her. However, SpongeBob notices something on her neck and pulls at it, revealing that Sandy's head was another mask and that the monster is actually Plankton. Plankton claims he was paid to scare everyone away and that he was just following orders. SpongeBob tells the police to "get the MONSTER out of his sight". The police take Plankton away and he drops a letter. It reads:
You have what you want.
Now clear out ALL of New Kelp City...
Do not fail me.
SpongeBob wonders who L is and Patrick arrives telling SpongeBob to spell the solution. SpongeBob spells out his name again and returns to his office.
Chapter 3: Two Puffs Too Many
SpongeBob is back at Chewy Louie's. The bartender is working there and SpongeBob asks him why there aren't any customers when it's lunchtime. The bartender guesses it might be because he let Patrick man the grill. The bartender decides to make SpongeBob a free Krabby Patty. SpongeBob thinks the patty looks delicious. The bartender flings him the bill saying that he "got ONE Krabby Patty for free... But this burger has 5 patties, 5 tomatoes, 23 slices of cheese..." SpongeBob interrupts him because he is frustrated about the burger being so big. SpongeBob's hat phone starts ringing again and he answers it. SpongeBob notes that there is something afoot at Snail-Po Headquarters. SpongeBob decides what to do with the Krabby Patty first. Patrick says that he would fling the burger to SpongeBob, but the burger breaks apart and Patrick resorts to asking SpongeBob if he wanted the burger TO GO. SpongeBob is irritated and heads to Snail-Po Headquarters.
At Snail-Po Headquarters, SpongeBob says that he has to keep a look out for any funny business, and that nothing is getting past him. A person wearing a crudely stitched up suit of Officer Puff arrives, saying that she is here to help guard the Snail-Po. SpongeBob tells "Officer Puff" to look out for anyone, being completely unaware that the person is not Officer Puff, even saying that "Her stitching looks lovely tonight". The sun goes down. It is midnight and there is still no sign of the thieves. Suddenly, the lights go out and SpongeBob asks if it is already bedtime. SpongeBob hears footsteps and looks around for the thief with his flashlight and sees Patrick. "Officer Puff" says that Patrick is the thief and that SpongeBob should catch him while she guards the Snail-Po and SpongeBob chases after him, after revealing Patrick, SpongeBob asks him what he is doing here and he talks about nachos. He also says that he works there. SpongeBob looks at the Snail-Po display case only to reveal it is missing, and since the fake Officer Puff was the only one else around, SpongeBob suspects the real Officer Puff is the thief. SpongeBob heads to Officer Puff's house.
When SpongeBob reaches Officer Puff's house he finds that the place has been ransacked. SpongeBob looks for clues and eventually notices something blocked behind furniture. He pulls away the furniture and finds a closet. SpongeBob opens it, revealing the real Officer Puff. SpongeBob tries to arrest her, but the fake Officer Puff comes in and greets the detective. SpongeBob asks how he can find out who the real Officer Puff is, and Officer Puff challenges the fake Officer Puff to see who can puff up faster. When the real Officer Puff puffs up faster, SpongeBob believes that she is real and pulls off the costume of the fake Officer Puff, revealing Squidward. SpongeBob wonders if it is Plankton again, so he pulls at Squidward's face, but it only hurts him because he is not wearing a mask. SpongeBob asks him where the Golden Snail-Po is, but like Plankton, Squidward doesn't know because he was following orders. SpongeBob asks who hired him and Squidward said he would tell him through a clarinet solo, but SpongeBob thinks his hat phone started ringing again and goes to answer it.
SpongeBob feels that his cases don't make sense, so he rethinks everything. He feels that all his cases are connected somehow. Thinking that he is overlooking something, he searches through his documents for clues, but it does not help him. SpongeBob then decides to take a trip back to the past, which is going back to other scenes and finding details that he (and possibly and very likely the player) missed. He notices that Larry spat out the golden flower instead of eating it at the office, that Larry was around when the monsters attacked and that he was quietly watching SpongeBob and Plankton while Plankton was getting arrested from an unseen location. He then looks through his clues in the clueboard: he wonders what Larry wanted to do with the Golden Flower, he thinks that Larry is too interested in the crimes when he looks at the photos (which are shown as "clues"), he notices that the criminal was a cat (or pretended to be) when he looked at the cat ears, he tries to guess who L is when he looks at the L letter and finally deduces that the criminal mastermind is Larry. SpongeBob leaves to find Larry.
SpongeBob wonders why there's no one around in New Kelp City, and why it's too quiet. Suddenly, he is ambushed by cats. Seeing a bag with balls of yarn, he flings the yarn at the cats. Seeing Larry through a window at a fancy restaurant, he enters it.
SpongeBob goes to arrest Larry, but it is revealed that the flower and Golden Snail-Po was used by Larry to take Precious on a date, and the monsters were used to make sure nobody else was around. SpongeBob is amazed by Larry and Sandy comes to take him back home. Patrick then spontaneously shouts that he was the bad guy all along. SpongeBob tries to explain to Patrick what actually happened, but gives up and closes the case.
Patrick is once again shown not to be very clever as he tells SpongeBob he is on TV, thus breaking the play's fourth wall as he is not supposed to know that SpongeBob is watching and he runs away from SpongeBob even though he should know he works at the Snail-Po Headquarters and is not the thief (even saying that he only thinks he works there).