In this episode, a new family from Utah moves into South Park, and their son Gary, stereotypically depicted as unusually perfect (achieving high grades, being perfectly polite, etc.), invokes the wrath of the other boys. Stan is drafted into the job of beating him up by the other boys, but Gary's sheer politeness leads Stan to discover himself walking away with an invitation to dinner that night. After dinner, the five-child, two-parent family has "Family Home Evening" where they play games, do performance art, and read from the Book of Mormon. Stan is intrigued and confused by all this, and asks his parents about the Mormon family's beliefs. His father concludes that they must be religious fanatics attempting to brainwash Stan, and heads over to confront them and beat them up (but only upon determining that Mr. Harrison is white). Instead, he too finds himself quelled by the family's perfection and politeness, and in the end, actually decides to convert to Mormonism himself. The next day, Kenny, Cartman and Kyle cruelly mock Stan for hanging around with Gary and his family, accusing Stan of going on a date with Gary. When the Harrisons and Gary show up, the three children walk off lying about going to "put in some volunteer work at the homeless shelter".
Throughout the episode, characters ask questions about Mormonism, and the story then breaks off to a sub-story about Joseph Smith and the founding of the religion. For satirical purposes, the show deviates from the original accounts of Mormonism's founding by adding extra to stories originally left vague (e.g. the precise location where Martin Harris lost the transcript of the Book of Lehi given to him by Joseph Smith); furthermore, during the narration, an upbeat tune plays in the background, with voices repeatedly interjecting "Dumb, dumb dumb, dumb, dumb" and "Smart, smart smart, smart, smart" at appropriate moments. The show asserts flaws in the religion's founding, which especially concern Stan (for example, that Joseph Smith offered no proof to the general public of finding the Golden Plates, and that he claimed to have translated from a slightly different plate after the first translation was lost while in the possession of Martin Harris). Stan ends up shouting at the Mormons that they're ridiculous for believing in it without proof; they smile patiently and explain that it's a matter of faith, while Stan argues that it should be a matter of empirical evidence. He further lashes out at them for acting unusually nice all the time, claiming it blindsides stupid people like his father into believing in Mormonism (to which Randy Marsh unwittingly responds "Yeah!"). Afterwards, Stan's family apparently chooses to convert away from Mormonism and goes back to Catholicism, at Randy's insistence.
Stan's anger doesn't much upset anyone in the Mormon family other than Gary, who confronts Stan and the other boys the next day. He points out that he believes his religion does not need to be factually true, because it still supports good family values. Gary condemns their bigotry and ignorance, stating:
"All I ever did was try to be your friend, Stan, but you're so high and mighty you couldn't look past my religion and just be my friend back. You've got a lot of growing up to do, buddy. Suck my balls."
He walks away, and the episode ends as Cartman (with a new-found respect for him) says, "Damn, that kid is cool, huh?".