The episode begins with SpongeBob waking up, and realizes that it's April Fool's Day. He then begins the day pranking Gary by saying they were going to be peasants and that they were going to have to move. He then pranks himself by saying that he was going to drink several glasses of lemonade, then goes to work. Squidward sees him and wonders what SpongeBob is happy about until he looks at the calendar, and realizes that it's April Fools' Day, which he says is SpongeBob's favorite holiday. Fearing the worst has to come (or so he thinks), Squidward calls Mr. Krabs saying he's sick and that he would not be able to make it to work. Mr. Krabs says that there is an art collector in his office who wants to buy Squidward's art and name him artist of the month. Squidward immediately rushes to the Krusty Krab, only to find that it was a silly prank by SpongeBob and Mr. Krabs. Squidward attempts to resign from his job, but SpongeBob persuades him to stay, promising not to pull any further pranks on him.
However, SpongeBob continues to prank the customers inside the Krusty Krab while hiding them from Squidward even though Squidward knows he is doing that. The customers seem to take SpongeBob's pranks lightly, because the pranks are considered funny and harmless. Although Squidward does not receive any more pranks as SpongeBob promised, Squidward gets annoyed over the SpongeBob and the customers' laughter. He decides to get revenge on SpongeBob by showing him what he feels is a "real" prank, and sets a rope trap with a blob of mustard in the middle.
SpongeBob goes to clean it up, and he gets his leg caught in the lasso. Squidward cuts a nearby rope, triggering a chain reaction which sends SpongeBob flying around the restaurant, colliding into several objects and areas, ending with him into landing in a garbage can. Squidward laughs hysterically at him and celebrates his victory, but a physically (as well as emotionally) hurt SpongeBob runs out of the restaurant in tears. Bewildered by SpongeBob's reaction, Squidward calls out to him, saying that he was just kidding, even turning to the customers for confirmation.
But the customers too are appalled by Squidward's prank, declaring that it was far too harsh to truly be considered "funny." They all leave the restaurant in disgust, with one of them angrily saying to him "April Fools, jerk" and another one yelling, "YOU STINK!" Squidward insists that it was only a joke (even saying, "Why is it every time I try to have a little fun, it's wrong?"), but as he looks around at the damage to the restaurant that his prank caused, and conversely realizes how SpongeBob was hurt during each part, it slowly dawns on him that SpongeBob's pranks were actually funny and meant to make people laugh, while his prank was cruel and meant to hurt and humiliate SpongeBob. Overcome with guilt, and realizing that the customers were right in that the prank was too harsh, he realizes that he has to apologize to SpongeBob for what he did.
Squidward goes to SpongeBob's house and sees SpongeBob's hat behind a rock. Assuming it's SpongeBob, he goes over to apologize, but then sees that it's just Patrick wearing the hat while digging. Squidward asks where SpongeBob is and Patrick tells Squidward that SpongeBob is in the house "impressed" (instead of depressed) and was crying a lot. Squidward feels even worse and attempts to apologize when SpongeBob answers the door, but since apologizing to others isn't something Squidward normally does, he initially finds himself to be physically incapable of saying something as simple as "I'm sorry."
Eventually, he is able to say it by putting a bubble over his head, so that SpongeBob does not actually hear his apology. Squidward walks away, saying that his conscience is clear, but is confronted by memories of what he did, feels guilty again, attempts to apologize to SpongeBob several unsuccessful times, and eventually goes back and genuinely apologizes to SpongeBob, but tells SpongeBob not to tell anyone. SpongeBob promises not to tell and forgives him, but then fully opens his front door, revealing that everyone else is inside behind him, and witnessed Squidward's apology.
They all say "April Fools!" to Squidward, who is flabbergasted by this. Squidward states that he was fooling them as well before running away to his house, while laughing maniacally.
This episode takes place before "Christmas Who?," which is why April Fool's Day is SpongeBob's favorite holiday, as he and the other Bikini Bottomites (with the exception of Sandy Cheeks) don't know that Christmas exists.
Telling Gary they were going to become peasants, and to eat salted shells instead of snail food
Telling himself he would drink dozens of glasses of lemonade for breakfast
Having Mr. Krabs call Squidward on the phone that an art collector from The Barnacle Bay Art Museum is at the Krusty Krab and wants to make Squidward artist of the month.
Putting a Whoopie Cushion on Mr. Krabs' chair.
Directing an old lady who asked him for a fork to the spoons.
Drawing a face on the back of his head and tricking a customer into thinking he was two different people.
Giving a customer one ice cube in his drink when he asked for a couple of them.
Telling his tongue that its shoes were untied.
Tricking Squidward into apologizing to him secretly in front of a room full people, including those who witnessed the prank at the Krusty Krab.
The line "You stink!" was first heard in "Pickles."
Squidward's Mom looks different than she does in "Krusty Towers."
The woman who asks SpongeBob where the forks are is the same fish that asks where the menu section is in "Neptune's Spatula." It seems as though she is in constant need of guidance but it's possible that it can be a coincidence.
When Squidward tries to apologize to SpongeBob for the first time, he says "I'm trying to say I'm..." and his head turns into a donkey and starts braying. A similar subliminal message also occurs in "Christmas Who?"
This episode and "Neptune's Spatula" only tend to air on April Fools' Day, as Neptune's Spatula is Fools in April's sister episode. However, recently, airtime of these episodes became a bit more common.
This is the second time that Squidward's hot water bottle has appeared. The first time was "Sandy's Rocket."
In Indonesia, after saying "This is an extreme thirst!," the scene usually goes straight to the scene where Tom wants a couple of ice cubes.
In the Polish dub, the episode's title is "Prima Aprilis" (April Fools).
After being pranked the first time, Squidward places his hat on Mr. Krabs's desk, but he has it in his hand when he leaves the Mr. Krabs's room.
Even after SpongeBob reveals to the old lady his prank of giving her a spoon rather than a fork, she still walks away with the spoon.
When the customers leave the Krusty Krab after Squidward's prank, they are all blue and brown finger shaped ovals.
After SpongeBob says "What" while Squidward is trying to apologize, the doorknob reappears even though SpongeBob took it down just fifty seconds earlier. However, it's possible that he put it back up.
When Squidward's head explodes while apologizing, neither his house or Patrick's house are there anymore.
When Squidward gives SpongeBob a message in a bottle, he puts a cork on it. However, as it rolls towards SpongeBob, the cork is gone.
When Squidward sees Patrick, the hat is down to Patrick's eyebrows. However, when Squidward says, "Why are you wearing that hat?!" the hat is farther up Patrick's forehead.
In one scene SpongeBob's holes were black.
Squidward finishes saying sorry before he stuck his tongue out.
In this episode, Bubble Bass is purple (or brown), instead of the usual green.
There is no possible way that many people can fit in SpongeBob's living room, and when Squidward was apologizing, he said that he "liked everyone" which means that maybe the whole of Bikini Bottom was in SpongeBob's living room. Unless it was the people just at the Krusty Krab and SpongeBob's friends, then they would fit into it.