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SpongeBob's Brain is the brain inside of SpongeBob's head. Depending on where it appears (including episodes, movies, and shorts), his brain can look and function quite differently.
Its first appearance was in "Plankton!" Here, Plankton invents a device that allows him to control others' brains. It works at least partially on SpongeBob's brain, although SpongeBob seems to still be in control of his thoughts and some of his actions. Here, his brain is dark pink, fairly small, and is not enclosed in a skull. Due to this, it can be seen to shake around when SpongeBob moves.
It next appears in "Scaredy Pants," where Patrick cuts SpongeBob's head down in order for him to dress like a round-headed ghost. His brain here is far bigger, a bit lighter in color, is split into two sections, and it seems to be more connected to him than its previous appearance.
Although it doesn't appear here in physical form, a picture of his brain is seen in "I'm With Stupid." It cannot be seen clearly, although it seems to resemble its appearance in Plankton!, other than being a lighter shade of pink.
The brain makes another appearance in "Welcome to the Chum Bucket," where Plankton is again involved. Here, he puts the brain into a robotic suit, and it seems to keep its personality even outside of SpongeBob's body. It is a lighter shade of pink here, and is less smooth-looking.
It briefly appears yet again in "Mermaid Man and Barnacle Boy IV." Here, the Bikini Bottomites go inside SpongeBob after they are shrunk by Mermaid Man's Belt, and they see some of his organs including his brain. It is again seen as two sections like a real brain, and is slightly lighter, but other than that it resembles its appearance in "Plankton!"
Although his actual brain doesn't technically appear in "Snowball Effect," 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. It is dark pink in color, making it comparable to its "Plankton!" appearance, but it is far bigger this time. SpongeBob appears fully functional even after it's out of his head; however, since this sequence was imaginary, it should not be taken seriously.
The next appearance of SpongeBob's brain is "Squilliam Returns." 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. It is not completely clear whether these rooms and mini SpongeBobs are real or just imaginary.
In the episode "Bummer Vacation" SpongeBob very briefly pops his brain out of his head to show mentally he can stay away from work.
In the episode "Night Light," it briefly appears when SpongeBob rolled his eyes in the back of his head just like in the episode "Plankton." It was when SpongeBob was afraid of the dark even inside of him, so then he put some light in his head.
Yet another appearance is in "Krabby Road." In this episode, 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.
It briefly appears again in "Bucket Sweet Bucket." In this episode, Plankton tricks Squidward, SpongeBob, and Patrick into helping him refurbish the Chum Bucket, and SpongeBob and Patrick get many of the supplies from the Krusty Krab. Among the supplies are water pipes; one of them goes through SpongeBob's head and gets out his brain. This time, it is quite small, and is an even lighter pink color. SpongeBob is barely functional without it here, and without his brain, he does nothing but make random sounds.
It once again appears briefly in "Penny Foolish." In this episode, the brain falls out of SpongeBob's head, and he chases it, showing that he can somehow survive without it. The brain also has the ability to squirt some sort of liquid at SpongeBob. It is again split into two sections, and is a light shade of pink similar to the previous appearance.
In "House Fancy," his brain makes a brief return. Here, it is revealed that Patrick had briefly borrowed SpongeBob's brain, and he gives it back to SpongeBob in the episode. The brain here is similar to the one in "Bucket Sweet Bucket," as it is very small and light pink, although this time it is covered in liquid as well. Strangely, SpongeBob is fully functional without his brain in this episode, unlike in "Bucket Sweet Bucket."
The brain's next appearance is "Stuck in the Wringer," although it again is only a brief appearance. When SpongeBob takes a shower, the water goes into his brain and cleans it, presumably because of SpongeBob's holes. It is a purplish-pink in color and appears fairly large, and, strangely, it actually has its own face in this episode. Washing the brain appears to make it happy.
Yet another minor appearances is "I ♥ Dancing." In this episode, SpongeBob claims to have music on his mind, and he takes his brain out of his head. It is literally playing music like a radio, and it even has a radio dial that SpongeBob uses to change the channel. This appearance of the brain depicts it as large, light pink, and split into two sections. SpongeBob is again functioning normally without his brain, although he is holding it at the time.
After years of only brief appearances, the brain makes another major appearance in "The Inside Job." Plankton again goes inside SpongeBob, hoping to get the Krabby Patty Secret Formula from his brain. The brain in this episode looks just like a brain version of SpongeBob's House, even including a brain version of Gary. However, it is revealed here that the formula is not in SpongeBob's brain, but his heart.
The brain also makes a appearance in A Day Without Tears when Squidward trying to make SpongeBob cry then it Shows the inside of SpongeBob's brain. The brain apparently has a large dam built inside it. SpongeBob's tears cause it to collaspe and the tears overflow the city of Bikini Bottom.
Yet another brief appearance is in "Kracked Krabs." In this episode, Mr. Krabs suggests that SpongeBob keep his brain peeled. SpongeBob reacts by literally peeling the top of head to reveal his brain. It is large in this appearance, and, while still light pink, is darker than its past few appearances.
The Brain yet again made a appearance in earworm when sandy was telling spongebob that he had a earworm in his head then it show The brain but it's not pink just like in the other's episode's are intended it blue.
In Whirly Brains, the whole episode is about it. For all the details, see Whirly Brains.
Its final appearance to date is in The SpongeBob Movie: Sponge Out of Water. Plankton once again goes inside 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.