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''.
* ArtisticLicense: Homer's so-called proof that God doesn't exist dips into ArtisticLicensePhysics and ArtisticLicenseReligion. Ignoring the possible AuthorTract behind it, God is not a number or a quantifiable figure (since Homer was talking to Ned Flanders we can assume Homer's referring to God as understood by Christians), so equations cannot be evidence against Him.
* BackAlleyDoctor: Moe, though he operates in his bar rather than a back alley. He even has cards of his shady business.
* BeliefMakesYouStupid: Savagely invoked. Homer uses his new found high I.Q. (which is actually 105, only slightly above average), 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. Cue Homer smiling when he finds out their stocks are down by 8 points.
* BittersweetEnding: Homer goes back to his old self and is happy again, but it comes at the cost of being unable to bond with Lisa like they used to.
* 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.
** A more subtle example can be seen in the [[https://frinkiac.com/img/S12E09/214339.jpg Classic Cartoon Commercials booth]], which is adorned by the artwork of Flatulent Fox, Brown-Nose Bear, Dinner Dog, Rich Uncle Skeleton, and Disgruntled Goat as seen in the episode "The Day the Violence Died".
* ContinuitySnarl: The idea that Homer proved God doesn't exist clashes with previous episodes (such as "Homer the Heretic") and subsequent episodes (such as "Thank God It's Doomsday") that acknowledge God's existence and depict Him, including The Simpsons Movie.
* 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 [whose I.Q is 150], the members of MENSA on "They Saved Lisa's Brain" who's IQ's range from 150 - 190 before Lisa joins [[note]]The Comic Book Guy, Lindsay Naegle, Professor Frink, and Principal Skinner[[/note]] and Martin Prince [whose I.Q. is 216, [[TheyWastedAPerfectlyGoodCharacter making him, despite the lack of acknowledgement, the smartest person in Springfield]] ]).
* 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.
* IsThisThingStillOn: After Homer demonstrates new animation techniques while wearing a MotionCapture suit, he goes into the men's room to relieve himself, while the audience can still hear and see everything he does. They cheer him on when he announces that the urinal cake has eroded away.
* 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.
* PersecutedIntellectuals: This episode showcases that even above-average intelligence is not accepted in Springfield--all entertainment in town aims for the LowestCommonDenominator and is proud to advertise itself as such and [[TallPoppySyndrome people hate Homer because they think he's lording his intelligence over them]].
* 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.
** Also a harsh one against religious people, particularly Christians and Jews as it's about God, see above.
** 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 ''WesternAnimation/{{Futurama}}'' and ''WesternAnimaton/FamilyGuy'', both of which suffered through ExecutiveMeddling and were initially canceled because of low ratings and shifting timeslots on FOX.