Act I
At an LDS Church Missionary Training Center, devout missionary-to-be Elder Kevin Price leads his classmates in a demonstration of the door-to-door method to convert people to The Church of Jesus Christ of Latter-Day Saints ("Hello!"). Price believes if he prays enough, he will be sent to Orlando, Florida for his two-year mission. However, he and Elder Arnold Cunningham, an insecure, compulsive liar, find out that they will instead be sent to Uganda as a pair ("Two by Two"). Price is sure he is destined to do something incredible, while Cunningham is just happy to follow ("You and Me (But Mostly Me)").

Upon arrival in northern Uganda, the two are robbed by soldiers of a local warlord, General Butt Fucking Naked. They are welcomed to the village by Mafala Hatimbi, where a group of villagers share their daily reality of living in appalling conditions while being ruled by the General. To make their lives seem better, the villagers repeat a phrase that translates as "Fuck you, God!" ("Hasa Diga Eebowai").

Price and Cunningham are led to their living quarters by Nabulungi, Hatimbi's daughter. They meet their fellow missionaries stationed in the area, who have been unable to convert anyone to the Church. Elder McKinley, the district leader, teaches Price and Cunningham thought suppression ("Turn It Off"). By the time they go to bed that night, Price is riddled with anxiety, but Cunningham reassures him that he will succeed and that, as his companion, Cunningham will be by his side no matter what ("I Am Here for You").

Price is confident he can succeed where the other elders have failed, teaching the villagers about Joseph Smith through a song that begins as a tribute to Smith but eventually descends into a tribute by Price to himself ("All-American Prophet"). The General arrives and announces his demand for the genital mutilation of all female villagers. After a villager protests, the General murders him. Taking every last measure to protect her, Hatimbi commands Nabulungi to stay in their house with all the doors locked and windows closed. She protests, insisting that the women of the village won't have to stay in hiding if they listen to the missionaries, as they hold the secrets to liberation, protection, and eternal happiness. Though her protests to go out and talk to them fail, she calms down after remembering how she was moved by Price's promise of an earthly paradise and dreams of going to live in that new land with all of her fellow villagers ("Sal Tlay Ka Siti").

The mission president has requested a progress report on their mission. Shocked by the execution and the reality of Africa, Price decides to abandon his mission and requests a transfer to Orlando. At the same time, Cunningham, ever loyal, assures Price he will follow him anywhere ("I Am Here for You [Reprise]"). However, Price unceremoniously dumps him as mission companion. Cunningham is crushed and alone, but when Nabulungi comes to him, wanting to learn more about the Book of Mormon and having convinced the villagers to listen to him, Cunningham finds the courage to take control of the situation ("Man Up").

Act II
When the villagers begin to get frustrated at Cunningham's teaching of the Book of Mormon and leave, Cunningham quickly makes up stories by combining what he knows of LDS doctrine with pieces of science fiction and fantasy. Cunningham's conscience (personified by his father, Joseph Smith, Hobbits, Lt. Uhura, Darth Vader, and Yoda) admonishes him, but he rationalizes that if it helps people, it surely cannot be wrong ("Making Things Up Again"). Price joyfully arrives in Orlando but then realizes that he is dreaming when his father questions him on if he left his mission companion. He is reminded of the nightmares of hell he had as a child and panics when his nightmare begins again ("Spooky Mormon Hell Dream"). During this dream he sees Jesus, Satan, Genghis Khan, Jeffrey Dahmer, Adolf Hitler, and Johnnie Cochran. Price awakens and decides to re-commit to his mission.

Cunningham announces several Ugandans are interested in the church. McKinley points out that unless the General is dealt with, no one will convert. Price, seeing the chance to prove his worth, sets off on the "mission he was born to do." After re-affirming his faith, he confronts the General, determined to convert him ("I Believe"). The General is unimpressed and drags Price away.

Cunningham concludes his preaching, and the villagers are baptized, with Nabulungi and Cunningham sharing a tender moment as they do ("Baptize Me"). The missionaries feel oneness with the people of Uganda and celebrate ("I Am Africa"). Price is seen in the village doctor's office, having the Book of Mormon removed from his rectum. Meanwhile, the General hears of the villagers' conversion and resolves to kill them all.

Having lost his faith, Price drowns his sorrows in coffee. Cunningham finds Price and tells him they need to at least act like mission companions, as the mission president is coming to visit the Ugandan mission. Price reflects on all the broken promises the church, his parents, his friends, and life in general made to him.

Nabulungi and the villagers perform a pageant for the mission president to "honor [them] with the story of Joseph Smith, the American Moses" ("Joseph Smith American Moses"), which reflects the distortions put forth by Cunningham, such as having sex with a frog to cure their AIDS. The mission president is appalled, orders all the missionaries to go home, and tells Nabulungi that she and her fellow villagers are not members. Nabulungi, heartbroken at the thought that she will never reach paradise, curses God for forsaking her ("Hasa Diga Eebowai [Reprise]"). Price has had an epiphany and realizes Cunningham was right all along: though scriptures are important, what is more important is getting the message across ("You and Me (But Mostly Me) [Reprise]").

The General arrives, and Nabulungi is ready to submit to him, telling the villagers that Cunningham's stories are untrue. She also explains that they will never see him again but protects his reputation in their eyes by saying a lion ate him. To Nabulungi's shock, they respond that they have always known that the stories were metaphors rather than the literal truth. Price and Cunningham arrive just in time to use Cunningham's lies of the latter being resurrected after being eaten by lions to scare the General and his men away. Price rallies the members of the Church and the Ugandans to work together to make this their paradise. Later, the newly minted Ugandan elders (including the General) go door to door to evangelize with "The Book of Arnold" ("Tomorrow Is a Latter Day"/"Hello! [Reprise]"/"Encore").