In a small church in Louisiana the congregation is about to sing a song, “Vaults of Heaven”. After the song, the preacher concludes his sermon, and the congregation go their separate ways (Overture). Poor Baby complains that “I Never Get What I Pray For”, before Poor Baby, Swallow and Brat meet Ed, who is about to drown some kittens. Swallow manages to save them and the kids realise that they should have been “Home By Now.” Earl is looking for a place to put up a tent for a revival meeting, where “folks go to dance with snakes” in order to test their faith in Jesus. Back at their home, their father Boone tries to convince them that “It Just Doesn’t Get Any Better Than This,” before recalling what his wife used to say: “Whistle Down The Wind.” As Poor Baby puts it, ‘Ma sang it better,’ and Swallow leaves to go feed the kittens, while singing “Whistle Down The Wind” to herself. In the barn, she prays that God will look after the kittens, but is startled by a loud cry, and a man jumps out at her. When she asks who he is, he only manages to moan “Jesus Christ..” before he collapses. She, Brat and Poor Baby promise they won’t tell anyone that he is there: “The Vow.”
In a bar where Ed is singing “Cold” to entertain the townspeople. The Sheriff arrives at the bar to warn the town that there is an escaped killer on the loose, and that he could be hiding out nearby. In the barn, The Man wakes to find himself surrounded by children, who all promise to take care of him and to keep his existence a secret. Left alone, he sings of “Unsettled Scores.” Later that night, Swallow brings him some food, and asks him if he will bring her mother back: “Being the Son of God, it can’t be that difficult for you!” She sings “If Only,” thinking of the way she wishes things could be.
Candy, a young black girl, and Amos, a white boy, sing of longing to get away from the town they live in, to a place they can be free: “Tire Tracks and Broken Hearts.” The townspeople sing of how the town used to be, and what it must be again: “Safe Haven.”
The children are discussing what it would mean if the mysterious man really was Jesus Christ, and what a difference it would make to their lives: “Long Overdue For A Miracle.” They realise that if they do everything right, they could save him, and that this could be the night “When Children Rule The World.” In the barn, they beg The Man to tell them a story, and he complies, telling them a story which he says will be in the next Testament, “Annie Christmas”. When he finishes, they ask repeatedly what the moral is, and when he admits that he doesn’t know, they offer him gifts and promise that “No Matter What,” they’ll always love him. The adults prepare to hunt down the escaped killer, their anger in complete contrast to the children’s innocence and happiness.
The townspeople are again preparing to hunt down the killer (Safe Haven Reprise). The Man asks Swallow to retrieve a package for him, 4 miles away at the train tunnel, and on noticing that she is shaking, tells her to “Try Not To Be Afraid.” Amos arrives at the barn to visit Swallow before he leaves town with Candy, and asks if she will tell him her big secret before he goes. He says if they share secrets, they’ll have to seal them with a kiss, and that “A Kiss Is A Terrible Thing To Waste.” The Man, hiding in the barn, overhears their conversations and joins in as Amos sings the song, realising that they seem to correspond to his life- “The emptiest words that there’ll ever be, it could have been me- it could have been me.” Swallow asks Amos to take her to the train tunnel before he can kiss her. There, she retrieves the package, but is almost killed by a train, though Amos manages to push her out of the way in time. “You saved my life, Amos! That means I owe you one now!” she says, then she tells him her secret: “What would you say if I told you Jesus had come back? He’s back, Amos! Jesus is in my barn!” They are interrupted by the Sheriff, who thinks he has discovered the killer, and is rather disappointed to find it is only Swallow and Amos. Earl has been hiding in the train tunnel the whole time and has overheard Swallow’s secret. At home, Swallow finds Poor Baby, who is upset because his kitten, which he asked “Jesus” to look after, has died; Swallow suggests they ask “Jesus” why he allowed the kitten to die: “If Only (Reprise).” In the barn, The Man tells them another story to explain why the kitten died: “Charlie Christmas,” saying that everyone dies in the end, “even the cat, even old Charlie…even your mother.”
On the highway, Candy waits for Amos: “Off Ramp Exit To Paradise,” but when he eventually turns up, its only to ask her where Swallow is, as he says she’s in trouble. When he runs off, Candy meets Earl, who says he knows Swallow’s big secret, and knows why Amos is rushing off in such a hurry. When he tells Candy, she decides to get back at Amos and Swallow by telling the whole town Swallow’s secret, interrupting the revival meeting: “Wrestle With The Devil.” The townspeople decide that the killer has to be found once and for all, in order to save the children: “The Hunt.”
Swallow runs back to the barn to warn The Man that the whole town are heading for the barn to catch him- when he says he will have to try and run for it, she begs him to stay, promising that she will protect him. He tries to make her realize that he is not the person she thinks he is: “Nature of the Beast.” But she says that she realizes that now, and simply needs him to be whoever he is. When the townspeople get to the barn, they find it surrounded by the kids who are determined not to let them hurt The Man. Swallow is trapped in the barn with him, and he says he will take her hostage, but quickly changes his mind and instead pushes her out of the barn to safety. Left alone, he sets fire to the barn, so that when Swallow manages to get back in, there’s no trace of him left. Swallow is convinced he hasn’t left for good, saying, “He’ll be back…I just know he will.” Her father tries to make her see that he wasn’t Jesus. She still isn’t completely convinced, asking, “But how do you know?” The family, together again, sing “Whistle Down The Wind.”