An airplane crashes and a funeral is held ("Prologue: Flying Machines in Pieces on the Ground"). At the funeral reception of a young woman who was onboard, a friend traumatized by her death has a seizure ("Titters"). This young woman, Bonnie, becomes depressed and is hospitalized when she falls into a coma.

The physicians don't understand the cause and put her on life support ("Doctor's Office"). Her lover, Alex, stays in the hospital and searches for alternative ways of healing her. Dana, the nurse, tries to comfort Alex, but he repeatedly turns her away ("Thanks, No").

Bonnie meets her Spirit Guide (in the form of a mouse) who entreats her to follow him. She does. Alex watches a tele-evangelical gospel healing program. In it, the Rev. Dr. Zackeriah Ezekhial Mobutsu heals Emma Jackson through song, prayer, Jesus and his touch. ("Get Rid of Religion!").

Alex meets Bonnie's mother when she comes to visit. It is awkward and they begin to argue ("He Said: She Said"). The Narrator only confuses things further.

Bonnie recounts her underworld trials ("It's Been Quite a Day (and i could use a drink)").

Alex begins work with a Christian Science practitioner, Mary Johnson. He introduces her to Bonnie's parents who are skeptical. The father misunderstands the practitioner's intentions and rejects her help. She offers her help to Alex nonetheless. He agrees to work with her. Alex shuts off Bonnie's life support. She continues to breathe. There is no explanation.

The Dr. Rev. begins healing at hospitals since he has been suspended from television on fraud charges. He blames his indictment on his racist superiors. Elmont escapes from the psych ward and tries to get money from people in the hospital. He eventually comes face to face with himself.

Alex confronts the Dr. Rev. as to whether he's a fraud. The Dr. Rev. explains he needs a plant to get the people to believe in him and then people actually are healed. The Dr. Rev. is impressed that Alex watches the show and agrees to heal Bonnie for $150. The Dr. Rev. gathers a group, and tries to heal Alex, an old man and finally Bonnie. Bonnie doesn't react at all. The old man doesn't react instantly, but then jumps up saying he can walk. A woman claiming to be his wife says he could walk before and that he's in the hospital for Alzheimers. The Dr. Rev. tells Alex to have patience and Jesus will heal her.

Alex is despondent. Dana tries to comfort him again ("The Virtues of Wrestling") and then turns into a water spirit. Bonnie dives into the river with the water spirits and learns the language in illo tempore ("ca ca tuve").

Dana helps Alex steal Bonnie from the hostpital to take her to see a shaman in Wyoming . He has trouble at the airport with a ticket taker ("Airline Counter") who won't let Bonnie onboard because she thinks Bonnie is dead.

We see Bonnie ascend further.

Alex arrives at the Indian reservation and is met by the assistant shaman, Wovoko, who is less than friendly. He is taken to the main camp and meets with the shaman. He is told that her spirit has been captured, but Alex can trade his spirit for hers in order to bring her back. He agrees to switch places with her.

The shaman holds a ceremony ("Journey Song") which climaxes in a seizure. The Narrator and Raoul (the Supertitles Man) try to translate. The shaman returns and tells Alex that Bonnie is not held captive. She is simply not coming back and he should go home. He goes to the airport and in desperation over doses himself with her medication.

He finds himself in her world. She sits in a chair in a vast desert in which only computerized camels trod. She has blindfolded the Spirit Guide and bound him in a chair which she has suspended in the air. She holds an unlit candle.

Alex asks why the candle she holds isn't lit and she recites the "Fire Regulations". Simultaneously, the Spirit Guide sings about how there are nearly no souls left in heaven due to the population explosion and his frustration in being unable to gain Bonnie's love "The Master Plan (of the Funki Mouse)".

She has been blinded in her ascent into the limitless. She appears to have lost her mind. She sings about the idea of numbers and absolutes in ("Pure Binary").

Alex asks Bonnie to come back with him. She declines. The Spirit Guide, himself unable to send Bonnie back, convinces the Narrator to bring her back as he's the only one with such power. The Narrator asks Bonnie to return and she agrees. The Narrator is terrified by the ease of this.

Alex and Bonnie spring to life in the airport. They sing a love duet ("Final Noise"). Alex sings of his love for Bonnie, Bonnie sings of the idea of Love. Others in the airport join Bonnie in song. The sound of the planes landing and taking off begin to drown them out. Bonnie receives a message from the white courtesy phone which we do not hear. Her jaw drops at the news. Finally there is only white noise