Mr. Mackey is now gluten-free and everyone is annoyed when he won’t quit preaching about how great he feels. But, after witnessing a disturbing demonstration of what happens to your body when you do eat gluten, South Park becomes the first town in America to go gluten-free.
After the events of the previous episode, "Go Fund Yourself", the boys return to school and, as revealed through dialogue(not shown in the previous episode), everyone now hates them. Before leaving previously, the boys had told everyone to "go fuck themselves". Wendy Testaburger is mad at Stan Marsh specifically because he broke up with her over the start-up company. Butters Stotch has gotten the brunt of it- not even allowed back in school because he burned down the gymnasium before leaving.
At the meeting to discuss Butters' action, Mr. Mackey gloats about his new dietary choice to not eat gluten, much to everyone's chagrin.
The boys, spearheaded by Eric Cartman, decide to have a party and make it about a cause, choosing Scott Malkinson's diabetes. However, when announcing it on a radio station, a few people complain about the party not having gluten-free foods.
Later, at the Community Center, John Garner tries to explain that the rumors of gluten being bad are simply false, by extracting gluten from dough made by wheat. Mr. Mackey baits him into drink the pure, concentrated gluten and eventually, the scientist complies. At first, it seems to have no effect, then suddenly, the scientist begins melting, sparking and having his penis fly off like a rocket, which puts the town in a state of panic.
Meanwhile, Kyle Broflovski is working on the party budget, when Cartman calls him in a panicked state because the whole town is burning the foods with gluten- and in turn the party cannot happen.
At the local farm, many of the townspeople watch the wheat farm burn down.
At the USDA, they are testing different dietary option to no avail.
At the Cartman Residence, Cartman is sick in bed because of there being no hope of a party. However, Kyle is still hopeful because they "still have Lorde", but it is revealed that Stan hasn't asked his father yet and leaves.
Meanwhile, at the Marsh Residence, the USDA finds a can of Pabst Blue Ribbon- which is made from wheat. Randy is then quarantined at Papa John's with an unnamed resident of the town and Mr. Garrison, feeding on toppings. Stan tries to ask his father about his co-worker who is supposedly Lorde's uncle, but cannot get an answer before being carried off.
Later, Cartman has a dream of Aunt Jemima in reference to Mother Abigail, from Stephen King's The Stand, who tells him that the pyramid is upside down.
Then, at Papa John's, the unnamed resident decides to eat the pizza dough and, at first, seems fine. The relief abruptly passes over however, when his penis flies off.
At the radio station, the boys, excluding Cartman, announce that they have canceled the party and instead tell everyone to learn about the dangers of gluten. Wendy calls out Stan, who breaks and reveals that they didn't get Lorde and didn't know what food to serve. Cartman calls Kyle, yelling again.
Later, Cartman calls the USDA and tells them that the pyramid is upside down so they turn the food pyramid upside down, changing grains from being at the bottom to the top and fats & oils from the top to the bottom. Much to the surprise of the scientists, it works.
The boys have their party with Scott Malkinson as a waiter. Cartman still sees Aunt Jemima and waves to her. Randy is conning as Lorde because he was lying about knowing Lorde's uncle, and Stan and Wendy reconcile.
AV Club gave "Gluten Free Ebola" a "C" rating saying: "Well, I’m glad we got to see Randy/Lorde at least, because without him/her, this was one of the dullest episodes of South Park in recent memory, with just a couple of gags sprinkled through a drag of a plot. It’s a bummer, because it started out pretty well, with the boys trying to re-assimilate after last week’s startup debacle. (“Doesn’t anyone understand the significance of ‘I’m sorry’ anymore?” was a great line.) And I loved where it felt like things were going, with Mr. Mackey as the prototypical gluten-hater who just won’t shut up about it."
IGN gave "Gluten Free Ebola" a "7.0" rating saying: "South Park's second episode in Season 18 started off with a fun carryover from last week, as the boys dealt with the fallout from their startup company in "Go Fund Yourself." Meanwhile, the overarching gluten storyline offered some laugh-out-loud moments -- including a staple town riot -- but the subject itself felt a bit dated. As for the boys' party, there wasn't much of a payoff, at least not in terms of connecting to the main story. The radio segments in particular were pretty dismal. Overall, "Gluten Free Ebola," while funny at times, lacked focus and didn't seem to know what it was trying to say."