Acte I
At the LDS Church Missionary Training Center in Provo, a devout, handsome, supercilious missionary-to-be, Elder Kevin Price, leads his classmates in a demonstration of the door-to-door to attempt to convert people to Mormonism Hello. One of the missionaries, Elder Arnold Cunningham, is an insecure, overweight, incorrigible nerd who tries to join in, but is completely hopeless. Price believes if he prays enough, he will be sent to Orlando, Florida for his two-year mission, but he and Cunningham are sent to Uganda as a pair Two By Two. After saying goodbye to their families, the Elders board a plane at the Salt Lake City airport. Price is sure he's destined to do something incredible (on his own), while Cunningham is just happy to have a best friend — one he met just the previous day You And Me (But Mostly Me).
Upon arrival in northern Uganda, the two are robbed at gunpoint by soldiers of a local warlord, General Butt-Fucking-Naked (an allusion to the real General Butt Naked). Mafala Hatimbi and a group of villagers share their daily realities of living in appalling conditions of famine, poverty and AIDS, while being ruled by a despotic, murderous chieftain. To make their lives seem better, the natives constantly repeat the phrase "hasa diga eebowai" and sing to the tune of a song composed around that phrase Hasa Diga Eebowai. Price and Cunningham join them in the song but are horrified to find out "hasa diga eebowai" translates to "Fuck you, God" in English and the villagers constantly blaspheme to cheer up.
Afterwards Nabulungi, Hatimbi's daughter, shows Price and Cunningham their living quarters where they meet the fellow missionaries stationed in the area, who have been unable to convert any native to Mormonism. Elder McKinley, the district leader, teaches Price and Cunningham a widely accepted method of dealing with the negative and upsetting feelings brought on by the challenges of Mormon life (including McKinley's own repressed homosexual thoughts), inviting them to "turn it off like a light switch" Turn It Off. The others agree their feelings must be hidden, at all costs. Though Price is riddled with anxiety, Cunningham reassures him he will succeed in bringing the natives to the church I Am Here for You.
Price is certain he can succeed where the other Mormon Elders have failed, teaching the natives about Joseph Smith, the founder of the LDS Church through a song that begins as a tribute to Smith but eventually descends into a tribute by Price to himself All-American Prophet. The natives do not show any interest in the slightest as they find religion useless and Price arrogant and annoying. Shortly after Price's attempt to dazzle the natives, General Butt-Fucking-Naked arrives and announces his demand for the circumcision of all female villagers by week's end, something that greatly angers the villagers; leading the General to execute a random villager to silence the locals' protests. Safely back at home, Nabulungi, moved by Price's promise of an earthly paradise, dreams of a better life in a new land Sal Tlay Ka Siti.
At the mission headquarters, Elder McKinley flies into a panic after he receives a message saying the Mission President has requested a full progress report on their heavily unsuccessful mission and his anxiety is only worsened after he learns of Price and Cunningham's failure. Shocked by the execution and dark reality of Africa, Price decides to abandon his mission and requests for transfer to Orlando while Cunningham, ever loyal, assures Price he'll follow him anywhere I Am Here For You (Reprise). However, Price unceremoniously dumps him as mission companion. Finding himself alone and heartbroken, Cunningham gains the courage to take control when Nabulungi comes to him, wanting to learn more about the Book of Mormon Man Up.
Acte II
Cunningham lacks much knowledge of the Book of Mormon, so he makes up stories by combining what he knows of Mormon doctrines with bits and pieces of science fiction and other cultural ideas, many of them unsavory Making Things Up Again. But Cunningham's creative stories relate to the problems of living in a war-torn Uganda, which gets the natives listening. Cunningham feels guilty for stretching the truth with the natives, but rationalizes: if it is to help people, it surely can't be wrong. While preparing to leave, Price reflects on the misdemeanors he committed in his childhood, including blaming the theft of a pastry on his brother Jack. He is reminded of the nightmares of hell he had as a child and he flies into a panic when his nightmare begins once again Spooky Mormon Hell Dream.
Price awakens from his nightmare and realizes it was wrong to abandon his post, telling the fellow Elders he re-commits to his mission. Cunningham arrives and announces ten eager Africans are interested in the church, and still stung by Price's rejection, he is unwilling to let Price back into his life. Listening to the promising news of success in the region, Price is inspired and sets off on the "mission he was born to do". Price confronts the General with the Book of Mormon in hand, determined to convert him I Believe.
Cunningham concludes his preaching and the villagers are enchanted; they are baptized and accept Mormonism, with Nabulungi and Cunningham sharing a tender moment as they do Baptize Me. The Mormon missionaries feel oneness with the people of Uganda, and celebrate I Am Africa. Price's attempted conversion of General Butt-Fucking Naked unfortunately does not succeed. Price drowns his sorrows in numerous cups of coffee at a cafe in Kitguli, where Cunningham finds him. He tells the bitter Price they need to — at the least – act like mission companions, as the Mission President and other senior Mormon leaders are coming to visit the Ugandan mission team to congratulate them on their progress. After Cunningham leaves, Price bitterly reflects over all the broken promises the Church, his parents, his friends and life in general made to him Orlando.
At the celebration, Price and Cunningham are singled out as the most successful missionaries in all Africa. Shortly thereafter, Nabulungi and the villagers burst in, and ask to perform a pageant to "honor [them] with the story of Joseph Smith, the American Moses" Joseph Smith American Moses, which reflects the distortions of standard Mormon doctrine and embellishments put forth by Cunningham. The Mission President is appalled, ordering all the missionaries to go home, and telling Nabulungi she and her fellow villagers are not Mormons. Cunningham becomes depressed because he ended up causing more trouble for the villagers and feels he is a disappointment to the Church. However, Price has an epiphany and realizes Cunningham was right all along; though scriptures are important, what's more important is ensuring religion helps people. Price and Cunningham reconcile as they reassure each other they will remain in Africa and help the Ugandans together, because they are best friends You And Me (But Mostly Me) (Reprise).
Nabulungi believes Elder Cunningham was making fun of her the whole time and tells the villagers he got eaten by lions. The General is about to take over their village with Nabulungi's help when the villagers tell Nabulungi the stories Cunningham told them as metaphors to help them in their daily life rather than literal truth; embracing Mormonism. Price returns with Cunningham and drive the General away, telling him you can't hurt the "undead." The missionaries reunite with the villagers and they all come together to evangelize "The Book of Arnold". Price rallies everyone — the Mormons and the Ugandans — to work together to make this their paradise planet, because, after all, they are all Latter-day Saints Tomorrow Is a Latter Day.