When the Simpson family visits an animation festival, Homer discovers Animotion, a motion capture technology that enables a real person to control a cartoon character with his or her own movements. Homer volunteers to demonstrate this technology and likes it so much that he invests his life savings in the Animotion stock. Two days later, he discovers that the stock has plunged and the company behind the technology has gone out of business. At Moe's Tavern, he tells Barney and Moe about his economic troubles, and Barney suggests that Homer become a human guinea pig to earn money.

Homer gets a job at a medical testing center. During one experiment, while commenting on Homer's stupidity, the doctors find a crayon lodged in Homer's brain from a childhood incident when he stuck sixteen crayons up his nose and was unable to sneeze one of them out. The doctors offer to surgically remove the crayon, and Homer accepts their offer. Homer survives the operation, and his IQ goes up from 55 to 105, allowing him to form a bond with his intelligent daughter Lisa. Homer's newfound brain capacity soon brings him enemies, however, after he performs a thorough report on the Springfield Nuclear Power Plant's many hazards, leading to massive layoffs when the plant is shut down until its many problems can be repaired or resolved.

When Homer visits Moe's Tavern, he sees an effigy of himself being burnt by his friends who worked at the plant. Homer realizes that due to his improved intelligence, he is no longer welcome and that his life was a lot more enjoyable when he was a moron. He therefore begs the test center doctors to put the crayon back into his brain. The scientists refuse to do it, but recommend Homer to someone who can: Moe, who is not only a bartender but also an unlicensed physician. At his bar, Moe inserts a crayon into Homer's brain, returning him to the idiot he was before. Lisa is initially saddened that she and her father have lost the new connection they shared. However, she finds a note written by Homer before the operation, explaining to her that while he is taking the "coward's way out," but that he has greater appreciation for Lisa after realizing what it is like to be smart like she is.

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