The episode starts with Marge and Homer tricking the kids into getting flu shots, giving them cute kittens to distract them while they drive to the hospital. Bart, however, is too fast and escapes from Dr. Hibbert's office before he can inoculate him. The doctor then makes it his sworn duty to give the boy a jab of the needle, as shown in a montage where he tries to get him at his school, at a funfair, and by plane in a ''[[Film/NorthByNorthwest North By Northwest]]'' homage. He eventually gets him by getting town drunk Barney to dress up as him and then rip his face mask off while the doctor takes advantage of Bart's confusion by jabbing him when he's unprepared. Bart then suddenly goes deaf as a side effect of the shot, unfortunately the annual teacher vs. student school donkey basketball game is coming up.

Before the game, a deaf Bart plays a prank on one of the donkeys by waving a carrot repeatedly in front of his face, then puts it in the back of his shorts, all while the national anthem plays. The donkey gets revenge on Bart by chewing his shorts off from the back just as the flag comes down, giving the appearance that he is mooning the flag. School photographer Martin takes a snap and eventually the picture becomes popular, with newspapers and subsequently the townspeople jumping on the idea that the Simpsons hate America, making the family pariahs as a result. This goes on for days and eventually Homer gets the idea to go on a popular talk show to prove that they don't hate the country.

While on the show, the host Nash Castor repeatedly tries to get the family to say that they hate America. Marge sarcastically says that if all Americans are loudmouthed talk show hosts, then she does hate America. Everyone reacts in shock. She tries to defend her case by saying that she is very well-liked in Springfield, then Castor uses that as an excuse to say that Springfield hates America, which soon catches on worldwide. The town's reputation having been ruined, Mayor Quimby gets the idea to rename it to "Libertyville", where people wear flag-themed clothing and all food is on sale for $17.99. During a patriotism-themed church sermon Lisa points out that people are being forced to love America, which goes against the foundation of the country. The family are then promptly arrested and put on Alcatraz for violation of the "Government Knows Best Act".

After days stuck in a small, lonely jail cell, a strange old man who touts himself as "the last registered Democrat" offers to help the family escape during a prison talent show where they sing an ultra-patriotic show. The audience are so distracted by the act that they miss the family escaping through a trap door below the stage. They dig up through the tunnel where they're being hunted in, and discover that the prison they're in is indeed on an island in a middle of an ocean. The family have no choice but to jump into the sea, where they come across a barge ran by French sea-farers, who rescue the family as they believe they hate America, just like them. The family enjoy their new life in France, but eventually decide that there's no place like home and decide to come back to America pretending to be immigrants to avoid a witch hunt.

The episode was universally panned by fans for its mean-spirited humor, disjointed storyline, and subtle-like-a-Louisville-slugger-to-the-back-of-the-head political satire. It has routinely ranked highly in lists of worst Simpsons episodes ever made, finishing in the top spot in 2009 and 3rd in 2011, with only season 11's "Kill the Alligator and Run" and season 21's "The Greatest Story Ever D'ohed"[[note]]the episode where The Simpsons go to Jerusalem on a religious trip and Homer deludes himself into thinking he's the Messiah after suffering from dehyrdation[[/note]] above it, though somehow it's manages to be better (or worse) than "Homer vs. Dignity" and "Saddlesore Galactica".

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!!This episode contains examples of:
* ArtisticLicenseHistory: Alcatraz hasn't been used as an actual prison since 1963, and these days, is a tourist attraction, so The Simpsons (along with Elmo, The Dixie Chicks, and anyone who opposes George W. Bush) should not have been locked away there.
* TheCatCameBack: Parodied with Dr. Hibbert's pursuit of Bart. It turns out they were several characters disguised as Hibbert.
* DrivenToSuicide: Homer mentions that Elmo hung himself in his cell.
* HalfwayPlotSwitch and RandomEventsPlot: So, uh... ''what'' exactly is the plot for this episode, again? It started with Bart going deaf from a bad innoculation and got hopelessly lost in heavy-handed anti-Republican sentiment.
* KafkaKomedy: The family become town pariahs after Bart accidentally moons the flag after a donkey rips his shorts off (although it did so as revenge for Bart torturing it with a carrot, which is pretty mean in the first place.)
* MyCountryTisOfTheeThatISting: The whole episode is an unsubtle satire of post-9/11 patriotism.
* NoodleIncident: [[SesameStreet Elmo]] is in Alcatraz because he "went to wrong fundraiser".
** [[ComicallyMissingThePoint And why is]] [[RiddleForTheAges Dr. Hibbert not allowed in the library anymore]]? All we know is that Moe did something to make that happen.
* TheOldConvict: The last registered Democrat.
* PatrioticFervor: Mercilessly parodied, to the point that it came across as a heavy-handed AuthorTract the likes of which would make ''WesternAnimation/FamilyGuy'' in its seventh season [[EvenEvilHasStandards blush]].
* PompousPoliticalPundit: The talk show host who interviews the Simpsons. He tells the audience to tune in next time to hear him talk louder.
* RepeatingSoTheAudienceCanHear
-->'''Homer:''' Hello? Appear on your TV show? Tell our side of the story? You'll see us there? [[ParrotExposition Goodbye? Dial tone?]]
* ShoutOut: The Simpsons escaping fleeing military surveillance while singing in public? You would expect them to sing [[TheSoundOfMusic Edelweiss]].
* TakeThat: At the overzealous patriotic attitudes of post-9/11 America during Bush's first term. The "Government Knows Best Act" is a jab at the controversial Patriot Act.
** The prisoners at Alcatraz include various people known for their opposition to Bush's America, including filmmaker MichaelMoore, the DixieChicks and (for some reason) [[SesameStreet Elmo]].