The family visits Wickerbottom's Pre-Nursery School, where Apu and Manjula are sending two of their octuplets. Homer and Marge have a talk with Dr. Hibbert about getting in, and decide to have Maggie go in. However, Maggie fails the initial screening because she cannot talk, until Lisa discovers some traits of intelligence. Maggie makes another screening. The results show that not only is Maggie brilliant, but her IQ of 167 is higher than Lisa's IQ of 159. Lisa is no longer considered "the smart one" of the Simpson family. Her attempts to find a new identity, including a goth girl named "Raven Crow Neversmiles", a cheerleader, a rapper, a soccer player, a cowgirl, and even a stand-up comedian, do not work out well.
At home, Lisa, in an attempt to prove everyone that she is smarter than Maggie, teaches Maggie false information. Marge, realizing this, scolds her for trying to sabotage her sister's education and that if that is how she really feels, then she should not be her sister's rolemodel. Heartbroken, she leaves the house and hides in the Natural History Museum, where there is no chance of Homer and Marge finding her, until Chief Wiggum, Lou and Eddie find her belongings in there. The family goes into the human body exhibit, but Maggie gets distracted and accidentally presses the swallow button, swallowing Homer, Marge and Bart. Maggie presses many buttons until she finally presses the evacuate button, following a visual cue from Lisa as to its color.
Ironically, after Maggie saves Homer, Marge, and Bart, she no longer has a secret to her intelligence — Henry (the owner of Wickerbottom's Pre-Nursery School) reveals a video tape of Maggie's audition and it turns out Lisa was showing her answers, which Lisa doesn't remember, but it is explained she subconsciously did that as she wanted Maggie to succeed. Henry starts criticizing Maggie which leads an angry Homer to start punching him, while Henry criticizes his punches until he is unconscious.
In the end, Lisa assures Maggie she doesn't care what anyone else thinks of her and that she is brilliant to her. However, Maggie plays Lisa's saxophone in the end, showing another sign of intelligence. A shocked Lisa reclaims her saxophone and tells her that "it's not for babies".
In the credits, Simon Cowell criticizes everyone who had worked on the show.