The episode begins with SpongeBob and Squidward cleaning Mr. Krabs' room, with Mr. Krabs telling them to watch over the formula. Meanwhile, Plankton is using an invisibility cloak to steal the formula, and ends up doing so when Squidward accidentally throws it out due to being in the trash. He goes back to the Chum Bucket to tell Karen this, and she becomes extremely happy.
SpongeBob tries to look for the formula, but can't find it. SpongeBob and Squidward look at the security footage to see what happened, and see that Plankton had stole it. They devise a plan to steal the formula back, while Plankton fails to open the formula due to there being a 12 hour time lock.
SpongeBob and Squidward go inside the Chum Bucket, right when Plankton finishes watching his show and goes to bed. After SpongeBob makes sure Plankton's asleep, they face many obstacles before eventually reaching the safe. However, whenever SpongeBob steps on a tile, he activates a trap which hurts Squidward. When they finally reach the safe, SpongeBob tries to take it, but this causes a rocket to take SpongeBob and Squidward and blast them outside of the restaurant.
Mr. Krabs comes back to the Krusty Krab, where SpongeBob and Squidward tell him that Plankton stole the formula. He gets very mad, but ends up stealing the formula back very easily by punching a hole through the safe outside the restaurant. The episode ends with Plankton mad that his formula is gone, while Mr. Krabs puts SpongeBob and Squidward in his safe to further protect the formula.
Karen's "kissy face" screensaver from "Grandmum's the Word" reappears when she kisses Plankton.
When Squidward turns on the Krusty Krab's security footage, a drawing of DoodleBob can be seen on the bottom of the table, referencing both "Frankendoodle" and "Doodle Dimension."
SpongeBob mimicking Plankton is a reference to "Mimic Madness."
Plankton turning into a genie when he is trying to open the Krabby Patty formula, which is a reference to "Spin the Bottle."
Squidward's claustrophobia from "Wishing You Well" is brought up again in the ending.
When Squidward turns on the Krusty Krab's security footage, the date 05-01-99 (May 1, 1999) can be seen on the bottom of the table. This is a reference to the airdate of "Help Wanted," the first episode of SpongeBob SquarePants.
The scenes from the horror movie Plankton was watching also appears in "The Legend of Boo-Kini Bottom" on on Karen's screen.
Plankton's bedroom in this episode is completely different from the bedroom he was previously shown with in "One Coarse Meal." Also, in "One Coarse Meal," Plankton sleeps in his bedroom alone, but in this episode, Karen and Plankton both share the same bedroom. As a result, "Bottle Burglars" is the first time that both Plankton and Karen are shown sleeping together in the same room.
This is the second episode to show Plankton's skinned form. The first is "Plankton's Regular."
When Spot chases after the fuel rod that SpongeBob threw, the lightsaber activation sound from Star Wars is heard.
The boat that falls on top of Squidward is the RMS Titanic, a British passenger liner that sank in the Atlantic after colliding with an iceberg on April 15, 1912.
