The prologue consists of two choruses, the "Chorus of Exiled Palestinians" and the "Chorus of Exiled Jews", each of which is a general reflection about the respective peoples and their history.

Act 1
Scene 1

The unnamed captain of the MS Achille Lauro recalls the events of the hijacking. Prior to that, most of the passengers had disembarked in Egypt for a tour of the Pyramids, and the ship set out to sea to return later for the touring passengers. The hijackers had boarded during the disembarkation. When the hijackers commandeer the ship, the passengers still on board are collected in the ship's restaurant. The narrative shifts to a Swiss grandmother, traveling with her grandson while the boy's parents are touring the pyramids. The ship's first officer, given the fictitious name of Giordano Bruno, informs the Captain that terrorists are on the ship and one waiter has been wounded. The Captain and First Officer try to keep the passengers calm. Molqi, one of the hijackers, explains the situation to the passengers at gunpoint. The Captain and Molqi have an encounter, where the Captain orders food and drink to be brought, and offers to let Molqi choose the food for the Captain to eat.

Scene 2

Following the "Ocean Chorus", another hijacker, Mamoud, keeps guard over the Captain. Mamoud recalls his youth and songs he listened to on the radio. The Captain and Mamoud have a dialogue, in which the Captain pleads that individuals on the two sides of the Palestinian–Israeli conflict could meet and try to understand each other. Mamoud dismisses this idea. During this scene is a passenger narrative by the Austrian Woman, who locked herself in her cabin and remained hidden throughout the hijacking. Act 1 ends with the "Night Chorus."

Act 2
The "Hagar Chorus", relating to the Islamic story of Hagar and the Angel and the Biblical story of Hagar and Ishmael is sung. It represents the beginnings of Arab–Israeli tension, of which the hijacking is one historical result.

Scene 1

Molqi is frustrated that he has received no reply to his demands. Mamoud threatens all of the passengers with death. Leon Klinghoffer sings, saying that he normally likes to avoid trouble and live simply and decently, but going on to denounce the hijackers. Another hijacker, called "Rambo", responds in harsh terms about Jews and Americans. The passenger, the British Dancing Girl, recalls how well the fourth hijacker, Omar, treated her and the other passengers, for example, letting them have cigarettes. Omar sings of his desire for martyrdom for his cause. At the end of the scene, Omar and Molqi have a dispute, and Molqi takes Klinghoffer away. The "Desert Chorus" follows.

Scene 2

Marilyn Klinghoffer talks about disability, illness, and death. She thinks that her husband Leon was taken to the ship's hospital, but he was shot, off-stage. The hijackers have ordered the Captain to say they will kill another passenger every fifteen minutes. Instead, the Captain offers himself as the sole next person to be killed. Molqi appears and says that Leon Klinghoffer is dead. The "Aria of the Falling Body (Gymnopédie)", sung by Klinghoffer, follows.

The "Day Chorus" links scene 2 to scene 3.

Scene 3

After the hijackers have surrendered and the surviving passengers have disembarked safely in port, the Captain remains to tell Marilyn Klinghoffer about her husband's death. She reacts with sorrow and rage toward the Captain, for what she sees as his accommodation of the hijackers. Her final sentiment is that she wished that she could have died in her husband's place.