While Kyle is honored for his acceptance of Caitlyn Jenner from President Barack Obama, Mr. Garrison observes that a large number of Canadians have entered the country illegally. When a group of Canadian students disrupts his class and causes him to use a racial slur, Garrison is sent to PC Principal's office and is forced to take a second language course to better understand his Canadian students. He daydreams while in class a song about the issues of the country, as he begins rallying people to his cause. Garrison interrupts a Canadian history play and expresses his true feelings to all the students and staff and gets fired by Principal in the process. This stirs tension between the American and Canadian students at South Park Elementary, and Cartman, Stan, Butters, Kenny, Token, and Craig decide that the only way to bring peace between them is to reenact the plot of The Lion King II: Simbas's Pride and have an American student "Hot Cosby" a Canadian student. Butters lost the not it game and was forced into the mission.
He begins rallying people to support him in building a wall on the border, threatening to "fuck 'em all to death" and "make the country great again."
Mr. Garrison has successfully gotten the entire town behind him to support building a wall, only to discover that the Canadians have already built a wall of their own on the border to keep the Americans out. Wanting to know what cool stuff they are hiding, Mr. Garrison sneaks into Canada in a barrel Niagara Falls New York.
Meanwhile, Butters has begun dating a Canadian girl named Charlotte. The two find themselves falling in love, and he is invited to dinner with her family. When asked why they left the country, her father explains that they and the rest of the Canadians left it unwillingly, the reason being that during the last Canadian election, there was a candidate who said outrageous things and never really talked about any actual solutions to the country's problems. None of the voters took him seriously and let him continue, which let him build momentum. By the time they wanted to get serious about the election, he had already been sworn into office.
Arriving at the border batterers and bruised from the waterfall, Mr. Garrison discovers Canada has become an almost post-apocalyptic wasteland due to their new president, and heads to his office. The two begin yelling at each other about their countries, before Mr. Garrison rapes the Canadian president so hard he dies. Once they hear news about his death, the Canadians all move back to Canada, separating Butters and Charlotte.
After his success at killing the Canadian president, Mr. Garrison tells the town that he will be joining the 2016 election to run for President of the United States, with his running mate, Caitlyn Jenner. The episode ends with Jenner and Garrison driving off, but not before Jenner runs over another young woman.
AV Club gave "Where My Country Gone" a "A-" rating saying: "And yet, I still got duped by last week’s episode, which I criticized for being a little too blunt, a little too one-sided. But after watching “Where My Country Gone?”, it’s clear that Trey Parker and Matt Stone have instated the PC Principal as head of South Park Elementary for a reason: His presence makes the academic hotbed—already a microcosm for so many sticky political and moral issues of the world—even hotter. In “Stunning And Brave,” it was the PC Police that got the brunt of the show’s satire. It was the PC Police who came out looking like fools, a joke that’s been told plenty of times before, even by the show itself. Now I see that the PC Principal (let’s just call him PCP from here on out) is there to make everyone look like fools. And South Park operates at its best when everyone—not just one particular group—looks like fools."
IGN gave "Where My Country Gone" a "8.0" rating saying: "This week's South Park improved upon the first, offering both scathing satire and a clear target: Donald Trump. With the help of both Mr. Garrison and Butters (and Canadian Donald Trump), "Where My Country Gone?" proved to be a surprisingly enjoyable entry, despite some muddled Kyle/Jenner callbacks from the premiere."