The episode begins at the Krusty Krab, where SpongeBob and Squidward are cleaning Mr. Krabs' office. Mr. Krabs tells them to clean the safe. SpongeBob has the combination to the safe.
Meanwhile, Plankton is outside the Krusty Krab, planning on stealing the formula. He makes himself invisible and walks over the Krusty Krab. Inside the Krusty Krab, SpongeBob is holding the formula like a baby. SpongeBob uses the trash can to lay the formula on. Squidward dumps the trash outside with the formula in it. Plankton now has the formula and takes it back to the Chum Bucket. Back at the Krusty Krab, SpongeBob notices that the formula is missing. He tells Squidward that he put it in the “circular file cabinet”. Squidward has to tell him that the item he placed it in was really a trash can, before they realize the situation in horror. They look all over the office. Squidward says that it's gone. SpongeBob went into tears at his mistake. They check the security cameras to see what happened to the formula. They found out that it was Plankton who took it.
Meanwhile, at the Chum Bucket, Plankton is trying to open the formula, but fails as there is a lock on the bottle cap that will only unlock after about 12 hours. Plankton then locks the formula in his own safe and celebrates his victory as he is prepared to finally open the formula the next day.
SpongeBob and Squidward decide to sneak into the Chum Bucket after Mr. Krabs closes and finds that Plankton is preparing for bedtime. The duo then starts to navigate to the safe, despite facing many impediments such as Spot, a sleepwalking Karen, and an electric eye that only detects and allows Plankton in. After SpongeBob uses a picture of Plankton to bypass the electric eye, they find the safe at the end of a hallway. Squidward tries to reach the safe, but he steps on a trap tile and gets smashed by a boot. SpongeBob tries to walk throughout the hallway but he activates more traps that only hurts Squidward. SpongeBob then takes the brutalized Squidward to the end of the hallway and opens the safe. However, as SpongeBob touches the bottle, an alarm goes off and sends him and Squidward into a rocket that sends them back into the back of the Krusty Krab. Mr. Krabs drives into the Krusty Krab to start a new day but finds SpongeBob and Squidward in a lot of pain from trying to get back the formula. Mr. Krabs finds out that Plankton stole the formula, but instead of getting very angry at SpongeBob and Squidward, he just breaks
Plankton opens the safe, but finds out that the formula has been stolen back. Spot is in the safe with a nuclear rod and proceeds to lick Plankton. Back at the Krusty Krab, Mr. Krabs decides to lock SpongeBob and Squidward into the safe so they can't keep their eyes off the formula again.
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.
