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.
* BeliefMakesYouStupid: Homer uses his new found high I.Q., among other things, to scientifically prove why God couldn't possibly exist. Flanders is, of course, angry, but after reading Homer's text through he quickly concludes he's absolutely correct. Instead of just accepting the other viewpoint Flanders then decides that he must prevent the others from ever seeing the document, though Homer is already putting it underneath every car's windshield wiper.
* BitingTheHandHumor: When Homer checks his stock numbers for Animotion, he shouts, "Yahoo!" which translates to "Yahoo!" (the website), and then says, "Huh? What is this crap?" which translates to FOX Broadcasting.
* CallBack: Ozmodiar, the space alien from [[Recap/TheSimpsonsS8E24TheSimpsonsSpinOffShowcase The Simpsons Spin Off Showcase]] briefly appears twice during this episode, once after Bart says cartoons do not have to make sense, and once more after all the employees are laid off from the plant.
* 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]]).
* CrossoverPunchline: [[WesternAnimation/{{Futurama}} Philip J. Fry]] appears briefly during the CouchGag.
* FailedASpotCheck: When Homer asks why the crayon in his brain wasn't detected earlier, Dr. Hibbert appears to explain that it was always hidden by his finger whenever he held up the X-ray.
* FlowersForAlgernonSyndrome: Homer experiences this.
* IntelligenceEqualsIsolation: According to Lisa, as intelligence goes up, happiness often goes down. She even made a graph of it.
* MixAndMatchCritter: The octoparrot, which Homer holds up as proof that the scientists are PlayingGod.
-->'''Octoparrot:''' Awk! Polly shouldn't be!
* NoseShove: How the crayon ended up in Homer's brain.
* RiddleForTheAges: How do you manage to disprove the existence of God ''accidentally''... while working on a flat tax proposal?
* TakeOurWordForIt: Homer's proof that there is no God. It even convinces Ned Flanders.
* 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 ''The Simpsons'', specifically ''Futurama'' and ''Family Guy'', 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]]).