SpongeBob runs towards Patrick's house, ready to go jellyfishing. Patrick says he'll go with him, but must put away his "secret box" first. Intrigued, SpongeBob tries to peek inside, but Patrick refuses to let SpongeBob see. SpongeBob entices Patrick by sharing his own secrets, but this only convinces Patrick to keep his secret box even more closely guarded. Even SpongeBob's various "secret" possessions fail to distract Patrick from the wonders only he can see.
As Patrick explains the lengths he must go to keep his box safe, he fails to notice SpongeBob sneaking off with it, giddily preparing to look. Patrick stops him just in time and struggles with SpongeBob over the box. The sight of SpongeBob's arms popping off while still desperately clinging to the box disgusts Patrick, making him question the validity of their membership in the Best Friends Forever Club. He threatens SpongeBob with the annulment of their friendship should he persist in trying to sneak a peak. Ashamed, SpongeBob begs Patrick for his forgiveness and promises to respect Patrick's right to secrecy. Placated, Patrick lets SpongeBob off the hook.
That night, SpongeBob cannot sleep, still thinking about Patrick's secret box and what could possibly be inside it. He convinces himself that by sneaking into Patrick's house to look while Patrick sleeps, he'll both spare Patrick's feelings and gain a secret of his own. Despite Gary's admonitions, SpongeBob puts his plan into action, heading out under cover of darkness, pulling on a silk stocking for a mask and slipping under Patrick's rock.
Inside, the box lays in full view on the sleeping Patrick's nightstand. Trying to tiptoe across a floor covered in potato chips and rubber ducks, SpongeBob fears waking Patrick with every step. Finally making it to the bedside, SpongeBob reaches for the box but Patrick sleepily grabs hold of it. SpongeBob gently slips himself in place of the box just as Patrick attempts to take something from it, yanking SpongeBob's tongue in the process. Patrick then places SpongeBob next to him on the bed, allowing SpongeBob to get back onto the floor. As he prepares to leave, SpongeBob trips on his shoelace and begins crashing and bouncing around the rock in a cacophony of noise, culminating in slamming against the wall and breaking a framed photo of him and Patrick in half. Despite all of this, Patrick remains fast asleep.
SpongeBob quietly remarks how heavy a sleeper Patrick is, which causes Patrick to finally wake up and catch the masked SpongeBob with the box. Thinking him to be the Clam Burglar, Patrick prepares to assault him with a pillow until SpongeBob reveals his identity with his Best Friends Forever Ring. In shock and distraught, Patrick declares their friendship to be over. The next moment, however, Patrick changes his mind and allows SpongeBob to go ahead and look. SpongeBob eagerly opens the box, only to find a mere piece of string ("A secret string!" as Patrick describes it). Thanking Patrick for letting him look, SpongeBob heads home, laughing at how he shouldn't have been surprised. Alone once more, Patrick demonstrates the true secret nature of the box: when the string is pulled, a secret compartment opens and reveals to Patrick an "embarrassing picture of SpongeBob at the Christmas party!"
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."
Gary is able to say the word "No" in this episode. This is the first time he has spoken a word, not counting his usual meows or "Ruff" in "Opposite Day since they're just sounds nor "Sleepy Time" since it was only a dream.
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.