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The episode begins with Jimbo and Chef in the Mayor's office, arguing about the South Park town flag: Jimbo wants to keep it, for it has been around since the time of their forefathers; Chef, however, insists it is racist. The South Park flag depicts four white figures hanging a black one on a gallows. The blatant racism incites Chef's indignation and leads him to believe that the whole town is racist. Chef immediately starts to rally support in order to change the flag. Neither he nor Jimbo can gather a lot of support, as very few townspeople have strong opinions on the issue.
In school, the class is assigned to debate the "Change the Flag" issue. Stan and Kyle lead the team that wants to keep the flag the same, while Wendy and Cartman lead the side that wants to change it (with Cartman only volunteering presumably to irritate Wendy). During lunch, Kyle and Stan ask Chef for help. Upon hearing that they think that the flag should be not changed, Chef gets agitated and verbally abusive towards the boys, who have no idea why Chef is so upset about the flag.
Wendy leads her team in the library when Cartman suddenly interrupts the process with his own strategy. He gets the team to dig up some dirt on Stan and Kyle, hoping to win the debate with ad hominem attacks on their credibility. Meanwhile, Kyle and Stan are at Kyle's father's law office. Kenny is killed when he eats 60 antacid tablets, believing they are mints, and then takes a drink of water, causing him to explode.
At the City Hall the Ku Klux Klan suddenly marches up, loudly voicing their support for the current flag as a symbol of "white power". This makes Jimbo, Ned and a number of the other flag supporters uneasy: they do not want to be sided on any issue with the Klan. To remedy this issue, Jimbo and Ned infiltrate in the clan and suggest that if they want the flag to remain unchanged they should advocate that the flag should be changed, because the majority of the people will always vote against what the Klan wants. The leader embraces the idea, and the Klan switches sides. Whilst leaving the meet they run into Chef, still wearing the Klan robes, Chef believes they are in fact KKK members, and drives off before in anger before they can explain.
The mayor cops out of the situation, deciding not to make the decision herself; the fate of the flag will instead be decided by the kids' debate. This puts a lot of pressure on Wendy, who, in their study sessions, suddenly begins to feel attracted to Cartman. This scares Wendy, because Stan is her boyfriend and she and Cartman actually hate each other. Bebe later explains the concept of sexual tension to her, advising that she should kiss Cartman just to get it out of her system.
During the debate, Wendy is totally distracted because she is attracted to Cartman and cannot deliver her opening remarks; she walks over and kisses him in front of the whole town, breaking the built-up tension. After this, she is able to continue her standpoint. When the turn of Stan's team comes, Chef and the rest of the adults find out that the children had not even perceived that the flag was racist, instead thinking that the issue at hand was capital punishment. Chef realizes that when the children looked at the flag, they only saw five people, with no regard to their colors, and is touched: he realizes that, in believing the whole town racist while throwing the slur "cracker" around, he was being the racist one. After Jimbo and Chef decide to come to a compromise, Kyle declares that they do not need to debate anymore.
In the end, ethnic diversity is added to the flag: the black man is now being hanged by a group of people of all races, including another black man, hand-in-hand. Chef delivers the moral of this story: his inclination to anti-racism almost made him a racist himself; perceiving things according to race leads only to further racism. In the final scene, Wendy says that she is glad that everything is over with and that her feelings for Cartman have disappeared. Cartman agrees and laughs nervously. Wendy runs after Stan, calling his name, leaving Cartman completely alone. After a few moments, Cartman sighs and walks away sadly, implying that he might have started to develop genuine feelings for Wendy.
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- Chef Goes Nanners Full episode at South Park Studios
- Chef Goes Nanners Episode guide at South Park Studios