Time: the present. Place: West Virginia. Three thrill-seeking teenage siblings (Rick, Ron and Ruthie Taylor) discover a half-bat, half-boy in a cave. After this "Bat Boy" bites Ruthie on the neck, they pummel the creature and take him to the sheriff of their small town, Hope Falls. A ghostly chorus sings of the extraordinary meaning of this pivotal moment in history (HOLD ME, BAT BOY).

The sheriff brings the creature to the house of the town veterinarian, who isn't home, but the vet's wife (Meredith) and daughter (Shelley) put Bat Boy in a cage (CHRISTIAN CHARITY). While they await the return of Dr. Parker, Bat Boy screams incessantly and refuses all food, and Shelley begins to have second thoughts about her new pet (UGLY BOY). While Meredith is in the kitchen trying to cook up something Bat Boy will actually eat, Shelley's boyfriend Rick comes over and, seeking revenge for Bat Boy's biting his younger sister in the cave, menaces him and leaves Bat Boy cowering and whimpering in the corner of his cat (WATCHA WANNA DO?). Meredith enters, angrily ousts Rick, and sends Shelley to bed. Meredith consoles Bat Boy by promising him acceptance and love (A HOME FOR YOU).

Meanwhile, the ranchers of Hope Falls admit in a town meeting that their cows are dying for mysterious reasons, and all of the townspeople at the meeting search for the potential cause, ultimately wondering if Bat Boy might have something to do with it (ANOTHER DEAD COW).

As a thunderstorm rages and the power goes out in Hope Falls, Dr. Parker finally arrives home from his goose-hunting trip. He is shocked by the creature he finds in his living room and drunkenly commiserates with Bat Boy, comparing the creature's condition to that of his own lifeless marriage. After a brief examination, the vet decides to put Bat Boy out of his "misery" with a lethal injection. As Dr. Parker is poised with the needle, Meredith enters and begs her husband not to kill Bat Boy. Dr. Parker agrees, but not before he extracts a promise from Meredith to "be a wife to me" (DANCE WITH ME, DARLING). Dr. Parker, overjoyed that there might be a chance that Meredith truly loves him again, then slashes the necks of the geese he has brought home and feeds Bat Boy the blood, which is exactly what Bat Boy needs to live.

As the mother of the injured girl demands that the Sheriff punish Bat Boy (MRS. TAYLOR'S LULLABY), the oblivious Parker family gives the remarkably intelligent and eager Bat Boy a full education. With the help of regular (and secret) feedings by Dr. Parker, Bat Boy quickly earns a mail-order diploma and transforms into an erudite and sophisticated young man, whom the family calls "Edgar" (SHOW YOU A THING OR TWO).

But the town finally delivers to Dr. Parker their concern about the "critter", and to keep them at bay Dr. Parker promises that Bat Boy will not attend the upcoming tent revival meeting (CHRISTIAN CHARITY - REPRISE). Bat Boy, however, desires to go out and see the world, and his passionate expression of this desire (A HOME FOR YOU - REPRISE) wins Meredith over. Knowing that her husband made a public promise to the contrary, Meredith nonetheless tells Bat Boy that she will take him to the revival meeting. When Dr. Parker angrily objects, Bat Boy reverts to his animal state and attacks Dr. Parker, knocking him to the ground. Meredith is overcome with concern - not for Dr. Parker, but for her dear "Edgar". Now Dr. Parker knows with certainty that Meredith, despite her recent softening toward him truly dow not love him, and, going mad, he privately vows to turn her feelings around - whatever it takes. While the town, Meredith and Shelley all express their hope that the revival will bring joy and renewal, Dr. Parker puts in motion his sinister plot. After taunting Bat Boy with a live rabbit, Dr. Parker steals away to the hospital, where he kills Ruthie Taylor with an injection (COMFORT AND JOY).

The next day, the Reverend Billy Hightower lifts the depressed spirits of the people of Hope Falls at the revival meeting (A JOYFUL NOISE). When Bat Boy, Meredith and Shelley arrive, the town is aghast - until Bat Boy wins them over with an ardent plea for acceptance (LET ME WALK AMONG YOU). The townspeople gather around Bat Boy and embrace him (A JOYFUL NOICE - REPRISE). But the uplifting mood is dashed when Dr. Parker arrives and tells the town that Ruthie Taylor is dead - and that Bat Boy's bit is responsible. Rick Taylor enters with a gun and threatens to kill Bat Boy, who attacks Rick and flees the scene. Dr. Parker then pretends to try to save Rick, but actually kills him with an injection. Now convinced that Bat Boy is a murderous freak, the town vows to find and kill him.

Dr. Parker has managed to turn the town against Bat Boy, but, in his madness, he has failed to turn Meredith's feelings around. As Meredith and Shelley search the woods for Bat Boy, Meredith convinces Shelley that their only hope is to find Bat Boy and move without Dr. Parker to a safe and secure location (THREE BEDROOM HOUSE). But when Shelley reveals that she has fallen in love with Edgar and wants to marry him, Meredith shocks her daughter by calling such an idea "hideous".

Shelley flees Meredith and eventually finds Edgar, who obviously shares her romantic feelings. But as the two awkward youth cannot find a way to express how they feel, the forest god Pan emerges from a nearby tree and calls upon all of the animals of the woods to show Shelley and Bat Boy how to love (CHILDREN, CHILDREN). While the angry townspeople continue to search for Bat Boy, the two young lovers repose in a post-coital bliss. Bat Boy, however, is now hungry, and Shelley tries to convince him to drink her blood (INSIDE YOUR HEART). But just as Bat Boy is about it sink his fangs into Shelley's arm, Meredith enters and calls their union an "abomination". When Bat Boy moves to attach Meredith for trying to keep them apart, Meredith blurts out a shocking revelation - one that makes Bat Boy and Shelley realize that they can never be together. Ever.

Bat Boy flees into the woods, finds a wandering cow, rips its head off and slakes his animal thirst. Bat Boy soliloquizes his despair to the bloody cow head he holds in his hands (APOLOGY TO A COW). The townspeople arrive and are about to kill Bat Boy when Meredith enters and begs them to spare Bat Boy's life. She promises that if they will only listen to the story she and Dr. Parker have to tell about Bat Boy's origin, they will understand why it is wrong to kill him. Dr. Parker and Meredith then reveal the astonishing tale, to the horror and disbelief of all assembled.

But the story only arouses more ire from the town, who scream for Dr. Parker to "kill the freak". Bat Boy, so devestated by the story he has just heard about himself, shocks Meredith and Shelley by agreeing with the mob - he wants to die, too. He goads Dr. Parker by calling him a coward and reveals the recent violation of his daughter. Despite the pleas of his wife, Dr. Parker is now ready to kill. With his knife, he slices his own neck open, causing Edgar instinctively to feed. With Bat Boy attached to his throat, Dr. Parker stabs him in the back. As Dr. Parker raises the knife for a second thrust, Meredith jumps on top of Bat Boy, and she receives her own fatal blow. Meredith and Dr. Parker fall to the ground, dead (FINALE: I IMAGINE YOU'RE UPSET).

Shelley catches Bat Boy as he falls, and she alone hears his final words, with which he renounces the world of humankind and chooses to embrace what he has obviously come to see as his better half: "I am not a boy, I am an animal." (FINALE: I AM NOT A BOY) Shelley mourns her loss, and the townspeople transform into a ghostly chorus, reminding us of the lesson of the play: "Don't deny your beast inside." (HOLD ME, BAT BOY - REPRISE)