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 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 everything is on sale for $17.76. 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.
This episode contains examples of:
- Actually Pretty Funny: Skinner brings up other times Bart has feigned illness for mischief, showing photos of Blind Bart, Wheelchair Bart, and Pregnant Bart. He then adds that his personal favorite is Railroad Spike-Through-Head Bart.
- Artistic License History: 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. Though it could be that all these prisoners are in some sort of underground facility that the tourists would not know about.
- The Cat Came Back: Parodied with Dr. Hibbert's pursuit of Bart. It turns out they were several characters disguised as Hibbert.
- Deus ex Machina: The French come to the Simpsons' aid as they are fleeing from Alcatraz. Not only do they save them from having to swim for hours and be pursued by the police, but they even pamper the Simpsons with fine cuisine and sumptuous fashion in Paris.
- Driven to Suicide: Homer mentions that Elmo hung himself in his cell.
- Dumbass Has a Point: Homer correctly advises Bart and his family to just apologize about the incident and not say anything else to make things worse. However, Marge has to ruin it.
- Enemy Mine: The French rescue and naturalize the Simpsons on the account that they must hate America because they've been thrown into Alcatraz and are escaping from it.
- Everyone Has Standards: Although he immediately twists it to his own benefit, even Nash Castor gives Marge (who almost always is an example of Women Are Wiser) a wide-eyed and wide-mouthed shocked stare when she is the one who snaps and says something on national television that will put the family in deeper trouble.
- Halfway Plot Switch: It started with Bart going deaf from a bad innoculation and then becomes a satire of post 9/11 Patriotism.
- Hero with Bad Publicity: The Simpsons become this and ostracized then imprisoned for apparently hating America and spewing anti-American sentiment.
- Hypocrite: The patriotic Americans claim their country endorses liberty and freedoms, but they're battling freedom of speech by locking up people with liberal, leftist opinions (including Bill Clinton) and demonizing whoever dislikes America. The Simpsons got locked up in Alcatraz just for controversial speech!
- Idiot Ball:
- Bart for not telling the people around him that his ears got swollen shut so they need to write down their messages to him, instead just trying to guess what they're saying by reading their lips. It's like he immediately adapted to living like a deaf person!
- Was it even a good idea for Homer and Marge to let Bart return to school without letting his ears heal first?
- Instantly Proven Wrong: A tenth of a second after Lisa gives a speech in church that America is built on the concept of free speech, and that this has all been an overreaction and people should be ashamed, federal agents burst through the church's windows and arrest the Simpson family at gunpoint for violating the "Government Knows Best" act.
- Kafka Komedy: 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).
- Morally Ambiguous Doctorate: Hibbert's first response to Bart developing an allergic reaction to the flu shot he gave him is not to do anything about it, but instead to swindle Homer into signing a document that will prevent him from suing Hibbert for malpractice and then run away.
- My Country Tis of Thee That I Sting: The whole episode is a satire of post-9/11 American patriotism, taking specific potshots at the American Republican Party. Despite the fact that the show has often mocked the United States and both Democrats and Republicans some Americans were not amused. Which is odd, because near the end of the episode The Simpsons do migrate back to the USA, because they miss it, despite everything that happened.
- No Indoor Voice: The conservative talk show host who brings the family on to frame them as anti-Americans. He even goes to commercial break promising to "talk even louder than this" when they return.
- Noodle Incident:
- The Old Convict: The last registered Democrat.
- Patriotic Fervor: Mercilessly parodied, since this episode aired recently after the 9/11 attacks, which triggered a strong wave of patriotism in the United States.
- Persona Non Grata: Thanks to Moe, Hibbert got banned from the library for reasons unknown.
- Political Correctness Gone Mad: The switch from Springfield to "Libertyville", including making everything themed with Patriotic Fervor to the point it's actually stupid and dangerous, like changing traffic lights to red, white and blue and apparently not keeping the red on the regular "stop" position, or changing all of the prices of items for sale in town to $17.76, which would only allow items like pizza slices to prosper.
- Pompous Political Pundit: Nash Castor, the talk show host who interviews the Simpsons (or rather, badgers them into saying something stupid by questioning them if they hate America). He tells the audience to tune in next time to hear him talk louder.
- Propaganda Machine: Lisa falls for the Schoolhouse Rock!-esque propaganda video at her re-education center because it's the first cartoon she's seen in 2 months.
- Pun-Based Title: On "Star-Spangled Banner".
- Rage Breaking Point: Marge can't tolerate the talk show host's constant instigation towards her family (he just asks them if they hate America and which part of it in specific, rather than allowing them to explain what happened with Bart which is the reason they were allegedly invited), so when she finally snaps she sarcastically says that she hates America and a lot of things in it, especially crappy talk show hosts. It puts her family in deeper water, eventually leading to them getting arrested.
- Random Events Plot: The episode begins with Bart going deaf and ends with the Simpsons in France, with a plot of Springfield changing its name to "Libertyville" in the middle. Need we say more?
- Repeating So the Audience Can Hear:Homer: Hello? Appear on your TV show? Tell our side of the story? You'll see us there? Goodbye? Dial tone?
- Shout-Out: The Simpsons escaping fleeing military surveillance while singing in public? You would expect them to sing "Edelweiss".
- Take That!: 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.
- Thought Crime: The "Government Knows Best" Act, which tosses the Simpsons in federal prison.
- A Tragedy of Impulsiveness: Marge getting fed up with Nash Castor and doing a sarcastic, angry rant on national television about how she hates America because it produces asshole TV hosts. Everybody on the set (even Castor) looks at her in shock and sure enough the family turns into pariahs.
- Tricked into Signing: Homer upon a malpractice waiver agreeing not to sue Dr. Hibbert.
- Wanting Is Better Than Having: Moving to France actually (eventually) gets the Simpsons fed up with stuff like eating bread all day long which makes them flee back to America... bear in mind, one of the show's running gags is Marge having a very deep desire to visit Paris.