It is Springtime in Bikini Bottom, and Patrick is emerging from his rock and storing away his Winter "coat" (sweater), burying it like a dog bone. SpongeBob, meanwhile, proclaims that he has "Spring Fever," and greets the flowers in his yard. When Squidward steps out of his house, SpongeBob asks him if he has said hello to the flowers as well. Squidward does so sarcastically, and the flowers hiss at him, causing him to run inside, terrified.
SpongeBob concludes that Squidward has "Hay Fever" and, as an act of kindness, decides to plant him some hypoallergenic flowers. He does so, and the moment he takes his eyes off of the flowers to grasp the watering can, he discovers it's been eaten. Surprised, he plants another one, which meets the same fate as he again reaches for the watering can. Determined, he plants another one and doesn't take his eyes off of it for 3 days. Patrick says Hi to SpongeBob, and SpongeBob looks at him and says the same thing. But after he looks at the flower again, it gets eaten. SpongeBob then discovers that the culprit is a green seahorse. SpongeBob is fascinated and imagines him and the horse riding together and decides to tame her.
Later, as he watches the seahorse, it is lured toward his floral bookmark, which it eats. They become friends and begin to ride around and do things together. As Squidward is biking to work the next morning, SpongeBob races past him on his seahorse, which he has named "Mystery." Squidward then rides off a cliff and causes a nuclear explosion when he hits the ground. When SpongeBob reaches work, he leaves Mystery outside at the bike post. Two fish approach Mystery and mistake her for a kiddy ride. One suggests the other to try it out, and when he inserts a coin into her "slot," Mystery kicks him into the distance, and he blows up on impact. The other fish runs away screaming, causing Mr. Krabs to come out and see what the trouble is. He sees Mystery and mistakes her for a monster; SpongeBob tells him she is his pet, but even though she is harmless to SpongeBob and not the others, he is ordered to get rid of her and if he disregards his order, he will be fired for not cooperating with him.
SpongeBob attempts to hide her in a cupboard in the kitchen until Patrick finishes building a stable. SpongeBob offers Mystery a Krabby Patty, which she begins craving after eating. After she craves, Mr. Krabs overhears this noise, and angrily comes in and confronts SpongeBob, threatening to fire him if he sees Mystery still here, but, however, he doesn't see her and leaves. After narrowly avoiding being caught by Mr. Krabs, SpongeBob realizes he has to be more careful. Squidward catches Mystery after an order goes missing, and Mystery goes on an eating frenzy while a crowd of customers became angry. Mr. Krabs finally catches SpongeBob nursing a sick Mystery in the kitchen, who is suffering from a stomach ache, now knowing that he had broken the rules. Mr. Krabs then becomes angry with SpongeBob and tells him that he plans to get rid of both, Mystery and SpongeBob. SpongeBob is responsible for breaking and disregarding the rule, but he pleads for mercy, explaining that Mystery is his friend and that he loves her.
Mr. Krabs, feeling sympathy for SpongeBob, tells him a story of his favorite dollar and how he eventually spent it for a soda on a hot day. He tells SpongeBob that Mystery needs to be freed because the indoors is not a place for a wild animal, and SpongeBob consents and takes Mystery out the front door where he painfully asks her to leave. He cries as she leaves without hesitation, he inadvertently tells Patrick to leave (believing it's still Mystery). Mr. Krabs comforts SpongeBob until Squidward shows him an empty safe. Realizing that Mystery ate the Krusty Krab's finances, SpongeBob and Mr. Krabs chase after her. The show ends with Patrick trying to get into a hat store, but the wooden plank nailed to his head blocks his way.
The "Three Days Later" time card has the same pattern as the "Squidville" title card.
Mr. Krabs would have obviously heard Mystery eating his money and noticed because Mystery's chewing sounds are considerably loud.
The Twelve Seconds Later time card is like the "Help Wanted" title card, except that it is orange in color.
Just like in "Jellyfishing," Squidward fell off a cliff, lands and explodes.
In Dutch, the title is called "Mystery," obviously inspired by the seahorse's name in the episode.
This is the second time a "3 days later" time card is used. The first "3 days later" time card was in "I Was a Teenage Gary."
Patrick with a wooden plank nailed in his head and SpongeBob's "imitation" of Mystery have become internet memes.
This is the second time Patrick has a board and a nail on his forehead. The first was "Life of Crime" in an original shot.
Running Gags: The onion bowl is making Squidward cry but then gets mad when he sees the it. The first time the bowl is on the ledge between the register and the kitchen. The second time the bowl of onions is on the register. The final time Squidward is shown pushing the bowl under the Krusty Krab customer so he won't be the butt of the joke anymore.
When SpongeBob and Mystery were dancing on TurboNick, a song from Nickelodeon's The Naked Brothers Band can be heard for an unknown reason.
This is the only time Scooter is seen exploding after he found the coin slot.
This episode shows the second time customers spitting out food after being disgusted while overhearing Mr. Krabs words to SpongeBob. The first was "Suds" where Mr. Krabs said "I don't want you sneezing all over my food" to him. In this episode, Mr. Krabs says "The kitchen is no place for a live horse."
In this episode Squidward says, referring to the Krusty Krab, "The food's no good here anyway," but in the episode, "Just One Bite," he enjoys Krabby patties, meaning that this episode takes place before that one.
Even though there is no reference to Christmas or anything related to that, this episode takes place after "Christmas Who?" because this episode takes place during the springtime, and takes place after "Help Wanted," and both "Christmas Who?" and "Help Wanted" take place on the same month.
The ending, where SpongeBob chases away Mystery, references to Harry and the Hendersons.
SpongeBob's refusal to set Mystery free despite Mr. Krabs' warning and SpongeBob eventually takes his boss's advice at the end of the episode is a reference to The Powerpuff Girls episode "Helter Shelter" where Bubbles refuses to free a baby whale despite Professor Utonium's warning that no animals should be brought home.
Among the things eaten by Mystery is SpongeBob's hat, but in a later scene, where he is attempting to give Mystery a bicarbonate soda, his hat is whole again.