Homer and Marge take the children to get their shots. Just before Dr. Hibbert is about to inject Bart, he escapes. After a chase through town and Hibbert being punched by Drederick Tantum for injecting him who then told him that the black off violence must end, Hibbert finally outsmarts Bart by having Barney and Moe impersonate him and the real Hibbert injects Bart. However, the shot makes Bart's earholes to swell shut, making him temporarily deaf. Hibbert also tricks Homer into signing a malpractice waiver.
While at the Springfield Elementary School donkey basketball game, Bart teases a donkey with a carrot, unaware that the school is reciting the National Anthem. After he places the carrot in his shorts, the donkey takes it and rips off Bart's shorts (just like his famous line "Eat my shorts"), thus exposing his bare butt. While Bart is bent over to keep his privates covered with his shirt, the U.S. flag is put up behind him and a photo is taken, which results in the crowd assuming that Bart is mooning the U.S. flag. Shortly afterwards, The Springfield Shopper takes the story and completely turns it around, making it seem as if Bart had deliberately mooned the flag. Soon, he and his family are hated by all of Springfield. Homer and Marge tried to clear up this misunderstanding, knowing it was an accident, but everybody refuses to listen, mistrusting Bart and his family.
Later, the Simpsons are asked to appear on a talk show and tell their side of the story. However, the host instead asks, "What part of America do you hate most?" (an example of the fallacy of many questions). Marge says that, if leading questions such as that are the only forms of discussion in America, then she does hate America. She also said she is well-liked in Springfield, prompting the host to say that Springfield hates America. Then the U.S. turns its back on Springfield, so Mayor Quimby frantically decides to change the name of Springfield to "Libertyville." Everything in town is quickly patriotized; the traffic light colors are changed to red, white, and blue, and everything costs $17.76. While at church, Lisa speaks her opinion about patriotism, and the Simpsons are taken into custody, in violation of the "Government Knows Best Act".
The Simpsons are taken to the "Ronald Reagan Reeducation Center", which houses Michael Moore, the Dixie Chicks, Elmo (who accidentally went to the wrong fundraiser), and Bill Clinton. With some help from the last-registered Democrat, the Simpsons escape the prison, but realize that the re-education center is actually Alcatraz Prison. While they are swimming to land, they are picked up by a French freighter and are brought to France. They are well adjusted, but still miss America, mainly because it is where all their stuff is. Then they move back to the U.S. dressed as 19th century immigrants from Europe, where Homer speaks of plans of integration into America.