It is the annual "Free Day" at the Bikini Bottom Zoo, and Mr. Krabs is abusing it by stealing light bulbs, filling an entire barrel at the soda machine, and raiding the gift shop with a fake mustache to hide his REAL identity. Meanwhile, SpongeBob and Patrick go to the Oyster Stadium to see Clamu the giant oyster perform tricks. However, Clamu is sleeping, making Patrick leave out of boredom. SpongeBob tries to wake Clamu up by throwing a peanut at her, and Clamu wakes up and goes on a rampage as she attacks people and cries in madness. SpongeBob believes himself to be responsible, and as he walks home with Patrick, Patrick decides to investigate the crime and is determined to discover the culprit and punish him.
At home, SpongeBob tells himself that the incident will blow over soon. However, when he turns on the TV, the oyster incident is the top news story. The Realistic Fish Head reports that the cry is so powerful that it can be heard all around the world (even above the surface), and asks what kind of "cruel, careless, evil person" would do anything to upset the giant clam.
Feeling guilty, SpongeBob goes to Squidward and Sandy for advice, but just like Patrick, both are concerned with finding and punishing the culprit, adding to SpongeBob's anxiety. To add more to his apprehension, once SpongeBob goes home, Patrick reveals that he found the bag of peanuts that the thrown peanut came from left near SpongeBob's home, stating that he's getting close to solve the mystery. Eventually, policemen enter SpongeBob's house and question him on the oyster incident. SpongeBob admits to everything they ask him, but instead of arresting him, they conclude from their evidence that Patrick is the culprit due to his stupidity.
Patrick is taken to Oyster Stadium, where he is chained to a platform in the middle of the stage and pelted with peanuts by the angry audience for the crime. Unwilling to let Patrick take the fall of something he didn't do, SpongeBob arrives at the stadium and orders everyone to stop throwing peanuts at Patrick. He finally confesses to having thrown the peanut, apologizing to Clamu, Patrick, and the people of Bikini Bottom and asking for forgiveness. The audience, refusing to accept SpongeBob's apology, decide to throw peanuts at both him and Patrick, but before they can do so, a zookeeper arrives and stops them, having captured Mr. Krabs with Clamu's pearl.
The zookeeper reveals that when Clamu was sleeping, Mr. Krabs stole her pearl, and when Clamu woke up after being hit by the peanut, she found out that her pearl was gone; thus it was the theft of the pearl, not the thrown peanut, that made Clamu angry and depressed in the first place. Having recovered the pearl from Mr. Krabs, the zookeeper gives it back to Clamu. However, the pearl turns out to be an egg as it hatches into a baby oyster.
Having being reunited with her offspring, Clamu finally calms herself down, which emotionally touches SpongeBob, Patrick, and the audience. With the truth of the crime finally revealed, SpongeBob and Patrick are cleared of all charges, and the audience turn their rage toward Mr. Krabs for stealing Clamu's offspring. Rather than admitting that what he did was wrong, Mr. Krabs instead makes the excuse that it's Free Day, and is literally buried in peanuts by the angry audience, much to his discomfort.
Clamu didn't cry suddenly after the peanut has been thrown at her. The pause might be the time Mr. Krabs took the pearl.
Alternatively, the pearl could've been taken while Clamu was asleep, and she noticed it was missing after she was rudely awoken by the peanut.
The zookeepers who attempt to calm down Clamu was later seen in "Born Again Krabs," as paramedics.
The countries that are seen outside Bikini Bottom are Egypt, The Netherlands, India, because of The Giza Pyramid, The Sphinx, and Taj Mahal.
The Realistic Fish Head mentions that other countries could hear Clamu's screaming, but if that was the case, then Bikini Bottom residents could have gotten deaf from it. It is possible the screaming is not that loud to the residents and they may hear it as regular loud screaming that could be heard from a distance.
The episode is a reference to a "smoking gun," a conclusive piece of evidence in a crime. The smoking gun, in this case, is the peanut.
The most notable "smoking gun" in American history is the piece of a phone conversation recording that mysteriously went missing in the Watergate scandal of the 1970s.
Clamu is a parody of the once popular and very famous whale Shamu in Seaworld.
When Clamu's loud wailing makes SpongeBob and Patrick fly to their seats, the peanuts in SpongeBob's bag flew out of the bag, but when Patrick said "Now this is a show!," his bag is full of peanuts again.
When SpongeBob knocks on Squidward's door, Patrick's house is nowhere to be seen.
Patrick's eyelids are usually purple. But when he says "Hey, SpongeBob!" when SpongeBob is trying to open his door, his eyelids are pink instead of purple.
When SpongeBob is about to go into his house after Patrick is saying he will investigate the lights are off but when he enters they are on.
This error happens again when SpongeBob says to Patrick "good luck with that."
It also happens when Patrick is arrested.
When the zookeeper pulls Mr. Krabs's pants off, his belt buckle colors are reversed to yellow on the inside and black on the outside, but in the next scene, the belt is back to normal.
At the end, some of SpongeBob's belt isn't completely filled in.