SpongeBob is running towards Patrick Star's House, ready to go jellyfishing. Patrick says he'll go with him, but must put away his "secret box" first. SpongeBob asks him what's inside the box, but Patrick refuses to let SpongeBob see. Despite repeated attempts, SpongeBob is unable to get Patrick into opening the box, even after he tempts Patrick with secrets of his own. All that is known is that whatever is in the box is extremely funny. SpongeBob eventually gives up and decides not to look. That night, SpongeBob cannot sleep, because he is too busy thinking about Patrick's secret box and what could possibly be inside it. So he gets out of bed and sneaks into Patrick's Rock and tries to sneak a peek while Patrick sleeps.
SpongeBob makes several loud noises, but Patrick doesn't wake up. However, SpongeBob quietly thinks out loud to himself that Patrick is a heavy sleeper, which causes Patrick to wake up and catch him in the act. He is shocked and declares their friendship to be over. But, Patrick ultimately forgives him and opens the box. Inside, there is just a piece of string ("A secret string!" as Patrick describes it). SpongeBob comments on how he "should've known," but when he leaves, Patrick reveals to the audience the real secret; when he pulls the string, a secret compartment opens in the box, and there is "an embarrassing picture of SpongeBob at a Christmas party" the audience doesn't see. Patrick then tells SpongeBob "Merry Christmas."
I can turn into a skyscraper!
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The sound effect heard when the box is falling on SpongeBob's knees can be heard in this episode accompanied with a Warner Bros. stock sound effect, on "Dexter's Laboratory," "The Powerpuff Girls," "The Powerpuff Girls Movie," and an episode of "My Gym Partner's a Monkey" called "Guano in 60 Seconds" despite Cartoon Network program's APM Music containings.
This episode reveals that SpongeBob and Patrick had been friends since they were babies.
The design of Old SpongeBob seen in SpongeBob's fantasy of Patrick and himself being old was used again in "Goo Goo Gas."
This episode's basic plot line bares a striking resemblance to the 'Dharma & Greg' episode "The Box" which aired just eight months before.
In the Polish dub, the episode's title is "Supertajne pudełko" (The Super Secret Box).
This episode as well as "Band Geeks" were the last to air before the 9/11 attacks, which occurred four days later.
In the 2005 movie War of the Worlds, Rachel, Tom Cruise's daughter, is shown watching the episode on TV. However, the audio and video are out of sync.
This is one of the few episodes to have just Tom Kenny and Bill Fagerbakke as the voice actors. Another one is "Rise and Shine."
Also, both this episode and "Rise and Shine" only feature SpongeBob, Patrick, and Gary as the characters.
Patrick's line "Duh!" and his face is a popular internet meme.
Patrick's line "The inner machinations of my mind are an enigma." and the milk spilling has become a popular internet meme.
A lot of scenes from this episode have been used on YouTube.
The end of the episode is foreshadowed earlier in the episode when Patrick pulls on SpongeBob's tongue, just like how he pulls the string on his secret box.
In Indonesia, SpongeBob didn't say "I've got a gazillion secrets!" Instead, he says "I've a Godzilla secret!," which means his secret is named "Godzilla secret."
Patrick says "Hands off, peeping Bob!," which is likely a reference to the phrase "peeping Tom."
When Patrick mistakes SpongeBob for the Clam-burglar, it is possibly a reference to a McDonald's character, the Hamburglar.
Squidward's house was missing near the end of the episode. This also occurs in "InSPONGEiac."
The potato chip on the floor that SpongeBob stepped on is in one scene, but in another scene, it is missing.
In this episode, SpongeBob is drawn in a lighter shade of yellow.
When Patrick says, "And to think we joined the 'Best Friends Forever' club?!" his purple eyelids disappear.
When SpongeBob gathers the "secret" stuff, he goes towards Patrick house, not his own.