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, Hibbert finally outsmarts Bart by having Barney (and briefly Moe) impersonate him and the real Hibbert injects Bart. However, the shot causes Bart's earholes to swell shut, making him temporarily deaf.
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. Marge and Homer try to explain to Skinner that Bart was deaf at that time; however, because Bart's history of pranks Skinner doesn't believe it. 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.
Bart and his family do not all hate America but when the family tries to clear up this misunderstanding, it is to no avail. Later, the Simpsons are asked to appear on a talk show and tell their side of the story. However, instead of listening to their side of the story as promised the host instead asks, "What part of America do you hate most?" (an example of the fallacy of many questions), also turning the question on Homer and Marge, the later of whom answers "Well America is not perfect". When the host asks if this is why the Simpsons hate Americans, Marge snaps, saying that if he is referring to loud-mouthed talk show hosts, which she notes "everyone seems to be in this country" (referring to the fact that questions such as that one are the only forms of discussion in America), then she does hate Americans.
This sentiment leaves everybody shocked, with even Bart, Maggie (who is too young to understand) and Homer (who is eating a sandwich) left taken aback by what Marge said. When the host expresses surprise that Marge has not been run out of town she replies that she is well-liked in Springfield, prompting him to declare that Springfield hates America. As a result, the U.S. turns its back on Springfield, even going so far to declare December 25th "We hate Springfield Day". 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 family 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's 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.