A sleepy Bart makes his way to the bathroom early one morning, unaware that Homer has rigged the toilet seat with Squat-N-Squirt, a novelty gag item that sprays anyone who sits on the toilet. Homer reacts with anger when Bart exits the bathroom without having triggered the device. Bart explains that he never sat down. A struggle ensues between Bart and Homer, and the Squat-N-Squirt shoots water in Homer’s face. Homer then turns on the shower nozzle, which sends water shooting everywhere. Marge demands to know what’s going on in the bathroom, prompting Homer to declare that he’s taking the whole family out for pancakes. As they head for the restaurant, the family passes a long line of parents and children assembled outside a neighboring building. One of those in line is Apu, who explains it’s application day at Miss Wickerbottom’s Pre-Nursery School. Homer gets in line with Maggie, determined to enroll her in the prestigious school. Inside the building Homer, Marge, Bart, and Lisa watch as a brutally honest interviewer questions Maggie, hoping to determine her intelligence level. The interviewer dismisses Maggie when he finds out she doesn’t talk. When the Simpsons return home, Lisa determines to prove that her sister is just as smart as the other kids at the school. She discovers that Maggie is quite bright. The Simpsons return to the school, where the interviewer gives Maggie an IQ test. Maggie aces the test, impressing the interviewer to no end. The interviewer meets with the headmistress, Miss Wickerbottom, and informs her that Maggie has an IQ of 167. Lisa is stunned when she hears the news, as her IQ is only 159.

When Lisa returns home, she decides it’s time to focus on improving her mind. Later she tells Marge that she’s used to being the smart one in the family, and now she’s having an identify crisis. When Lisa returns to school, she decides to try out new identities. Her first is stand-up comic, which bombs miserably. Next she tries going Goth, but that also fails. She tries a variety of new personalities, but none seem to fit. Meanwhile Marge and Homer take Maggie to the pre-nursery school, where Miss Wickerbottom shows them the proper way of praising their daughter. Later, at home, Lisa offers to help Maggie with some flash cards, only Lisa mischievously teaches Maggie the wrong answers. Marge catches her in the act. She tells Lisa that Maggie needs a different role model. A sobbing Lisa runs upstairs. That night Lisa experiences a dream in which she pushes an adult Maggie, who’s confined to a wheelchair, down a flight of stairs. A horrified Lisa awakens from the dream. She decides to run away from home.

When the Simpsons realize Lisa is missing, they turn to Chief Wiggum for help. Meanwhile Lisa takes refuge inside the Springfield Natural History Museum. After the museum closes for the day, Lisa visits the various displays, including a lunar landscape and a Visible Man atrium. She makes her way inside the Visible Man’s mouth and lays down on the tongue. She takes out a photo of her family and grows homesick. Meanwhile the Simpsons embark on a search to find the missing Lisa. Wiggum informs the family that police discovered Lisa’s backpack and blanket inside the Visible Man mouth. The Simpsons make their way to the museum and begin searching the various exhibits. Lisa spots them and hides. Wiggum shows the family where Lisa’s belongings were found. Marge places Maggie on a chair next to the control panel that operates the Visible Man exhibit. Then she, Homer, and Bart enter the mouth area. Maggie begins playfully hitting the buttons and knobs on the control panel, including one labeled “swallow.” The tongue rises and the Simpsons fall backwards into the throat. They end up trapped inside the stomach. Wiggum tells the family that the only way out is for the baby to press the red “evacuate” button. Homer, Marge, and Bart ask Maggie to press the button, but she responds by hitting a green button marked “digest.” Juices begin filling the stomach. Homer decides to use reverse psychology. He tells Maggie to hit the yellow button. Unfortunately she follows his instructions and hits the yellow button, which is marked “churn.” The family is then tossed around by the stomach walls. Lisa runs up to Maggie and tells her to press the red button. Maggie immediately pushes the red “evacuate” button, shooting the family through the intestine area. They land in a fountain on the museum’s ground floor. Later Lisa wonders why Maggie didn’t press the correct button until she told her to. Miss Wickerbottom and the school interviewer appear. They replay a tape of Maggie taking her IQ test. It turns out that Lisa subconsciously fed Maggie the correct answers as she took the test. Lisa realizes the baby isn’t a genius after all.