It is mentioned and seen in Squidward's thoughts. When SpongeBob and Patrick claim they will knock each other's brains out in a snowball fight, Squidward imagines the scenario, in which Patrick throws a snowball at SpongeBob and his brain falls out.
The inside of SpongeBob's brain is seen in this episode. Inside, there are miniature figures resembling SpongeBob, and there are areas resembling an office and a bathroom. When Squidward pretends to own a five-star restaurant, the miniature SpongeBobs delete all of SpongeBob's thoughts and memories so he will only think about being a successful waiter.
Plankton has a device that is able to play music from different formats; one of them is "brain," and, in hopes of hearing a song about the Krabby Patty secret formula, Plankton connects SpongeBob's brain to the machine. This results in SpongeBob singing the music selected from the machine dial.
The brain falls out of SpongeBob's head by Mr. Krabs' search of SpongeBob's 'penny'. They both chase after it, showing that SpongeBob can still move and function without it. The brain also has the ability to squirt some sort of liquid at SpongeBob.
When Squidward tries to make SpongeBob cry, the inside of SpongeBob's brain is shown. The brain apparently has a large dam built inside it. SpongeBob's tears cause it to collapse and the tears overflow the city of Bikini Bottom, being a metaphor for SpongeBob being no longer able to hold in the tears.
Plankton once again goes inside of it, and it once again is dark pink and smaller. Inside the brain is a gigantic space with SpongeBob's extremely happy thoughts, including the popsicle twins. This huge amount of happiness drives Plankton insane.
This episode revolves around SpongeBob's and Patrick's brains. They both use their own brains as Whirly Brains, an invention where one's own brain can fly and be controlled in the same way that a normal person would to a remote-control helicopter.
When SpongeBob enters the Empty Head Society, he removes his brain by detaching it from its stem. This causes him to act similarly to the other members of the society, but he still retains some of his intelligence because his stem is intact. He tries to water his brain stem, but this causes it to burn out. SpongeBob remains without his brain until Patrick brings it back to him. His brain is shaped like a cube throughout this episode.