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 previously said that animals could be ginger to Cartman's disbelief; however, Cartman claims to have seen a red cow since that exchange. Craig asks where he found the red haired cow.
When he shows the other kids the cow he had found, it is clear that Cartman has dressed the cow to look ginger, which only Kyle realizes.
Over the world, many news stations report on the discovery of the ginger cow. This leads to mass suicides due to the heifer supposedly bringing about the "end of times."
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, despite the fact that they speak perfect English. The rabbis explain 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 that instead of destruction and death, the red heifer may in fact 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 finally 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 in order to keep Cartman from revealing the truth.
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't true, as proven in "Good Times with Weapons" and "T.M.I."). With peace destroyed, Cartman taunts Kyle with a fart "dessert" (whipped cream and a cherry) smeared across his face. Kyle is left looking at the floor, dejectedly.
AV Club gave "Ginger Cow" a "B+" rating saying: "As with nearly every episode this season, “Ginger Cow” is bursting with too many ideas and not enough time to harness them into a single, coherent episode. But whereas past episodes had a couple of half-decent ideas that rarely went anywhere, this episode has six or seven really great things to explore and spends more time lining up real-life footage to cheer on David Lee Roth than delve deeply into any of them. Kyle’s dream in which God may or may not have praised his actions is a good example of this. Was this in fact a real visitation, or simply a byproduct of Kyle’s ego? Stan’s opinion of Kyle starts to nosedive as the latter gets more zen, but it’s clear onstage in Jerusalem that Kyle still has his wits about him even while in the throes of self-sacrifice. I’m not particularly upset that we didn’t learn one way or another if God actually spoke to Kyle. But I’m a little annoyed the Stan/Kyle schism didn’t have enough narrative room to breathe. Both of them are right. Both of them are wrong. But neither really gets a chance to generate friction with the other via their opposing viewpoints. Ideas are never this show’s problem. But choosing which one gets primary focus often is."
IGN gave "Ginger Cow" a "7.5" rating saying: "All said and done, South Park: "Ginger Cow" had a lot going for it in terms of concept, and this episode certainly hammered on a topic well worth discussing. Unfortunately, 22 minutes wasn't quite enough time to say all that needed to be said."