After losing the family's life savings in the stock market, Homer gets a job as a test subject for scientific experiments, one of which reveals the true reason behind his stupidity: a crayon that got stuck in his brain when he was a child. When Homer gets the crayon surgically removed, he becomes a more intelligent man -- and soon learns that being smart doesn't equal being happy.
!!This episode contains examples of:
* AffectionateParody: Of ''Literature/FlowersForAlgernon''.
* BackAlleyDoctor: Moe, though he operates in his bar rather than a back alley. He even has cards of his shady business.
* BitingTheHandHumor: When Homer checks his stock numbers for Animotion, the stock name for FOX Broadcasting is "Huh, What Is This Crap?", which is down eight points.
* CrapsackWorld: Homer seems like a super-genius with the crayon removed from his brain. However, he later states his new IQ is 105, which is only slightly above average. The people of Springfield are ''just that stupid'' (including the ones said to be smart, like Lisa, Martin Prince [whose I.Q. is 216], and the members of MENSA on "They Saved Lisa's Brain"[[note]]The Comic Book Guy, Lindsay Naegle, Professor Frink, and Principal Skinner[[/note]]).
* IntelligenceEqualsIsolation: According to Lisa, as intelligence goes up, happiness often goes down. She even made a graph of it.
* TakeThat and ArsonMurderAndJaywalking: When Smart Homer walks the streets looking for a place for smart people, he passes by places catering to idiots and morons, like Lunkheadz, The Dum-Dum Club, and The Disney Store.
** Marge's line about how animated shows seem to be everywhere -- or were, last year, is yet another burn on the animated DuelingShows that tried to be better than ''TheSimpsons'', specifically ''Futurama'' and ''FamilyGuy'', both of which suffered through ExecutiveMeddling and were canceled because of low ratings and shifting timeslots ([[HilariousInHindsight Ironically, Family Guy was revived in 2005 and is still on FOX, with reruns airing on local stations, TBS, and Cartoon Network. Futurama, on the other hand, reran on Cartoon Network and was revived for Comedy Central, only to get canceled again, but it does live on in reruns and on DVD and Matt Groening is trying to revive the show again]]).