The episode begins with Principal Brown breaking the news about Darwin passing the aptitude test with perfect scores. Since this had never happened before, Brown informs the Wattersons that Darwin has been sent to a government institute for geniuses to have his brain experimented on. The entire family is clearly very upset about this, especially Anais, who claims that the whole operation seems to be a form of quarantine. Brown is intrigued by her insight and wonders if there is another genius in the room, which scares Anais into acting like a fool. Nicole is outraged at this and questions Brown about the ethics of taking her son away from her family, but Brown claims that Darwin is only registered as a "pet fish." and bluntly states that they will never see him again.
Gumball vows to be accepted into the institute as well, which causes everyone else in the room to laugh mockingly. Gumball leaves Principal Brown's office and goes to the schoollibrary to try and study. Meanwhile, Richard and Nicole are outside of the school crying over Darwin, when Rocky comes up to them, carrying a suitcase. They ask what the suitcase is for and Rocky explains that he is having rent problems and does not want to stay with his parents. He asks Nicole and Richard if he can stay at their house for a while, which they allow, but on one condition. Back at the library, Gumball runs into Colin and Felix, who inspire him to inflate his head. After accidentally spitting all over them, he meets Bobert who is surfing the internet. He encourages Gumball to try using "the largest source of information in the world" which Gumball attempts but is unable to open up the browser without Bobert's assistance. After he finally clicks the icon, the sheer magnitude and size of the internet causes his memory to overload; meaning he had to be rebooted by Bobert.
Still trying to make himself smart, Gumball looks around the library and sees Teri, Leslie, and two books, reading books. Gumball finally realizes what he has been needing to do this whole time, watch a book. He finds a book, and sits in between Carmen and Carrie, who are both studiously reading. Gumball attempts to watch his book but needs to ask Carmen for help. She is annoyed by him not knowing that he is supposed to read books, and leaves after explaining this.
Meanwhile, at the house, Rocky is dressed up with fins, green pants and shoes (like Darwin), and Nicole and Richard attend to his every whim. As Rocky wonders why he is wearing the clothes they gave him, Nicole creepily tells him to call them mom and dad.
As Gumball struggles to read, his brain literally decides that it has had enough and leaves through his ear. Gumball pleads his brain not to go, as he cannot possibly pass the test without it. His brain tells him that it is stupid, after which Gumball decides to train him. This kicks off a training montage with Gumball's brain training itself physically until it becomes strong. Gumball and his brain confronts Brown to take the test, but the brain knocks out Principal Brown with a lamp. Later, at the house, when all hope seems lost, a guilt-stricken Anais reveals that she filled out Darwin's aptitude test. Some clipboard men come to return Darwin after they found out Darwin was not the one who had filled out the aptitude test and demand they give them the real genius. To protect Anais, Gumball's brain says that Rocky filled out the test, and they take him away. At the very end of the episode, Rocky is seen being begged to solve an equation, but refuses to do so until he gets everything he wants.
Darwin is rarely seen in this episode, and only has one line of dialogue, despite the plot being about him.
A "Gluteus Maximus" is a muscle that makes up the shape and appearance of the posterior, which means Gumball was called a butt.
In this episode, the other Wattersons do not know that Anais is a genius, yet in "The Goons," they all seem to be fully aware of this. The only logical explanation is that "The Genius" chronologically takes place before "The Goons."
During the training montage, Gumball shows pictures of famous scientists for Gumball's brain to break. One of these is a picture of Charles Darwin, who is Darwin's namesake. The other two are Albert Einstein and Stephen Hawking.
After Gumball's brain crashes, the Macintosh SE/30 startup sound is played.
Towards the end of the episode, when Gumball's brain tries to convince the clipboard men that Rocky is the genius, Gumball tells them his brain is "insane in the membrane," a reference to Cypress Hill's 1993 hit "Insane in the Brain."
When Anais tells the family that it was her who filled out Darwin's aptitude test, Gumball's whiskers vanish.
The speaker tells Darwin to write the answer with a dry erase board marker when the board clearly had chalk.
In the episode "The Gi," Gumball was seen using the Internet, but in this episode, he does not know what it is.
When the Wattersons and Principal Brown laugh at Gumball, Principal Brown's tongue is missing and Anais' mouth is discolored.
When the family says "Rocky?" the ink on Darwin's face disappears, then reappears when they go to the front yard.
When Gumball peeks at the eggheads through the library shelf, his eyebrows are gone. Also in that same scene, Gumball's nose is discolored yellow.
One of the clipboard men removes the face of the other to see a warrant, but in the next scene, the clipboard man's face is back on.
When the computer crashed, it incorrectly spelled Programme (British spelling of "program") as Programe.
When Nicole said "What makes you think I'll let you take away my son?!" a quarter of Richard's right ear is missing.
When Gumball goes past Bobert while leaving a trail of saliva, the line on Bobert's right side is gone.
After the researchers tell Rocky that he would be able to live at their research center for free, the popcorn he is holding in the subsequent shot is not rendered properly.
When Gumball is on the internet, his whiskers are missing.