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:
* FiveFiveFive: Moe's surgeon card has the phone number 800-555-1000.
* 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 a voice-controlled programs 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".
* 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.
* HypocriticalHumor: Homer is amazed by the burning effigy at Moe's until he realizes it represents him.
* ImprobablyHighIQ: Inverted; Homer states his post-surgery IQ is only 105 (100 being average). One could just take his apparent intelligence as being compared to the rest of his town, but he still does things which would require objectively high intelligence, like somehow mathematically disproving the existence of God.
* 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.
* ItRunsOnNonsensoleum: God's existence is disproven--in a way that even Flanders immediately understands and believes--by a mathematical proof contained on one piece of paper (that Homer calculated while filing his taxes).
* 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 ''slightly'' 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:
** 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 ''WesternAnimation/{{Futurama}}'' and ''WesternAnimaton/FamilyGuy'', both of which suffered through ExecutiveMeddling and were initially canceled because of low ratings and shifting timeslots on FOX.