Religious leaders descend upon South Park to witness a Biblical prophecy that has been fulfilled. Cartman and Kyle are the only two at odds as the world embarks upon a thousand years of peace and harmony.
While the other students are eating lunch in the South Park Elementary Cafeteria, Cartman comes through the entrance and publicly apologizes to Kyle, whom Cartman had ridiculed earlier. Kyle had said that animals could be ginger and Cartman did not believe him; however, Cartman claims to have seen a red cow since that exchange.
When he shows the other kids the cow he had found, it is clear that Cartman dressed the cow to look ginger, which only Kyle realizes.
Over the world, people see the small local news story about the cow, which leads many to commit suicide.
The next day, Kyle is called to the Principal's office. There are two rabbis who Principal Victoria and Mr. Mackey need Kyle to translate. The rabbis reveal that the red heifer, the cow, means that Armageddon is here. Kyle tries desperately to stop this and reveal that it was a prank by Cartman, but to no avail.
Later, leaders of Islam, Christianity, and Judaism discuss what is and what is not allowed in the Armageddon until one Muslim suggests the red heifer may mean the end of violence in the Middle East. Everyone else agrees and it is set in stone. They sacrifice the cow in Israel by dropping it from a helicopter onto a building and peace is made.
Once Kyle sees this on television, Cartman comes by and says that he has to tell the truth, but Kyle pleads and begs him not to. Cartman suggests that he will not say anything if Kyle were to, perhaps, insult his mother, which Kyle reluctantly does.
Later, at South Park Elementary, in order to prevent Cartman from destroying world peace, Kyle becomes Cartman's servant. He even forces himself to ask Cartman to fart in his mouth, which Cartman gladly does. Later, in Mr. Mackey's office, Kyle states he likes Cartman's farts. As he says so, Cartman walks into the office to give him more farts, as Mr. Mackey watches on, confused.
In Jerusalem, the religious leaders join their faiths' symbols into one, the Van Halen symbol, thus ushering in ten years of Van Halen.
In South Park, Stan asks Kyle about his love of Cartman's farts and, after a less than convincing argument as to why, recruits Kenny in order to find out what's going on.
That night, Kyle hallucinates a big, glowing orb that tells him to shave his head and be peaceful about what he is doing, which Kyle does.
The next day, at South Park Elementary, Kyle is again taking Cartman's farts. Stan and even Butters try to get him to stop, but he does not, instead saying that he is taking the punishment for the greater good. Later, Stan tells Kyle that he can suck farts, but he should not be stuck up about it.
In Israel, with Cartman ready to give Kyle more farts, Stan tries to announce that the red heifer was a prank. However, Kyle stops him and Stan makes up a story of how he saw red heifer come down from the sky. Unfortunately, the Hebrews from earlier reveal that the prophecy was that a fat kid with a small penis would make a cow look ginger, making Kyle's 'sacrifice' entirely pointless. Even though this is true, Cartman denies it and says that he has a huge penis (which isn'ttrue). With the peace destroyed, Kyle looks depressed as Cartman gives him a fart with whipped cream and a cherry.