ACT ONE: The setting is New York City in the summer of 1947, though much of the action takes place in flashbacks. The opera begins with the Narrator. He's actually one of the main characters, Stingo, grown older and looking back at his youthful experiences. He introduces the story by describing how he arrived in New York from his home in the south, hoping to become a writer, and moved into a Brooklyn rooming house.
As the action begins, we meet one of Stingo's fellow residents. Sophie Zawistowska is a striking, young Polish woman, first seen while she's arguing with her boyfriend, Nathan Landau. Nathan hurls insults at Sophie, then ridicules Stingo as well, and storms off. Stingo tells Sophie that, from what he's seen, she's better off without Nathan.
But Sophie tenderly recalls how she and Nathan first met, and the episode is presented in a flashback. Sophie goes to a local library, where she's berated by the librarian after getting poet Emily Dickinson's name wrong — asking instead for works by "Emil Dickens." Humiliated and feeling sick, Sophie faints, and a charming Nathan comes to the rescue. He takes her home and fixes dinner — introducing himself as a research biologist.
With the flashback over, Sophie tells Stingo that Nathan is a warm person at heart, and simply has a touchy side and a bad temper. As they say goodnight, Stingo asks where she got the number tattooed on her arm. "Oswiecim," she says. "Auschwitz." Before long, Nathan returns and begs Sophie to forgive him.
ACT TWO: Nathan and Sophie knock on Stingo's door, and ask him to come with them on an excursion to Coney Island. Before agreeing, Stingo demands an apology from Nathan, who sheepishly complies. Nathan and Sophie dress up in 1930s costumes for the occasion and the three leave together — but not before Sophie breaks up another argument, about injustice in the American South.
As the summer goes on, the three friends grow closer. Stingo begins writing a novel, and agrees to let Nathan read the book as it progresses.
Sophie is more forthright with Stingo than she has been with Nathan. Earlier, she talked about her happy family life in Poland. She has described her gentle and caring father, a law professor, and the two children she had with her husband, who was one of her father's loyal students. But now she tells Stingo the real story.
During another flashback, Sophie is with her father — an anti-Semite who dictates his writings to her. In one diatribe, he calls for the, "abolishment of the Jewish element from Polish society." Then, in a flash of inspiration, he orders Sophie to strike the word "abolishment," and replace it with "extermination." Sophie tells Stingo that her father was a brutal man. When both he and her husband were killed by the Germans, she says, she felt no grief at all.
Their conversation is interrupted when Nathan arrives, excited by a research breakthrough at his lab. He's also enthusiastic about Stingo's book, and raises a toast to Stingo as, "the next great American writer."
ACT THREE: The opera's Narrator, the aging Stingo, looks back on 1947 and describes his growing devotion to Nathan. He also admits that he fell deeply in love with Sophie, and was haunted by stories of her wartime experiences.
In a flashback, Sophie is with her friend Wanda, in occupied Warsaw, in 1943. Wanda is a member of the resistance and urges Sophie to join the effort, as well. Sophie speaks perfect German, and could use her skills to translate documents stolen from the enemy. Sophie refuses. Both her husband and her father have been executed by the Germans. She's on her own, with two children to care for, and can't take the risk.
But the Narrator then reveals that, despite her caution, Sophie was arrested for smuggling food into the city. She and Wanda were both sent to Auschwitz, where Wanda was tortured and killed.
In another flashback, we see Sophie working as a typist and translator for the camp's commandant, Rudolf Höss. He's attracted to her, and takes brutal advantage of her helplessness as a prisoner.
After Höss has a discussion with the camp Doctor about the use of sick inmates for forced labor, Sophie begs the commandant for his help. She's desperate to have her son sent away from Auschwitz to a camp where he can be "re-educated" as a loyal German. Höss agrees to have her son relocated, and Sophie is overjoyed.
The flashback ends, and the scene returns to 1947, in the early autumn. Sophie and Stingo are in a Brooklyn bar, waiting for Nathan. Sophie says Höss didn't keep his word. She never saw her son again, and doesn't know whether he survived the war or was killed in the concentration camp.
When Nathan arrives Sophie greets him lovingly — but he's angry. He makes a scene, accusing Sophie of infidelity, and ridiculing Stingo's novel. He says he's through with both of them. Before he leaves, he brutally insults Sophie one more time — wondering out loud what she, "the beauteous Zawistowska," must have done to survive Auschwitz while so many others died. With Nathan gone, Sophie is left feeling totally alone and turns to Stingo for comfort.
ACT FOUR: Nathan's brother, Larry, has asked Stingo to come and visit him. He tells Stingo that Nathan's life is basically a lie. He's not a research biologist — he barely manages to hold down a meaningless job in his firm's library. He's never been to Harvard, as he's claimed, and holds no college degrees at all. Larry says Nathan may be a genius, but he's also insane — diagnosed with paranoid schizophrenia. Larry feels sorry for Sophie, who doesn't know any of this. He asks Stingo to keep an eye on Nathan, and report back from time to time. Stingo is stunned by this news and says he'll try, but that Nathan seems to have disappeared.
Back at the boarding house, Stingo gets a phone call. It's Nathan. At first he seems cheerful, but then he accuses Stingo of sleeping with Sophie. Sophie overhears, and tries to take the phone, but Nathan crudely refuses to speak with her. Stingo won't give up on Nathan, and wants to know where he is. Nathan says he's close by, and he'll be coming for both of them. Then, before he hangs up, he fires a pistol shot close to the receiver.
Afraid for their lives, Sophie and Stingo take a train south, stopping in Washington, D.C., where they find a hotel. When Sophie wonders how she'll survive without Nathan, Stingo offers himself as the solution. He tells her they can go to his father's farm in Virginia. Stingo then admits that he loves her, and wants them to be married. Sophie says he's sweet, but she can't possibly do that. Then she tells him the one story about her past that's she's never told anyone before.
In one, final flashback, Sophie and her two children arrive at Auschwitz. Confronted by the camp Doctor, she begs for their lives. They're Polish, she says, and not Jewish. They're Catholic, and both the children speak German. In that case, the Doctor says matter of factly, he'll grant her a privilege: She can keep one of her children. At first, Sophie doesn't understand. The doctor makes it clear. She can keep only one child. The other will be taken away and executed. She must choose which child she will keep, or both children will be killed. Helpless, and desperate with grief and fright, Sophie tells him to take the younger child, her daughter. The girl screams as she's dragged away.
Back in reality, Sophie tells Stingo that as the child was taken, she was holding a favorite toy — a doll. Since then, Sophie has been unable to bear the word "doll," or to speak it in any language.
Sophie falls into Stingo's arms, and their embrace becomes passionate. But in the morning, Stingo wakes up alone. Sophie has left a note, saying that she has to find Nathan, whatever that may mean, and she may not see Stingo again.
Stingo returns to Brooklyn, and the boarding house, where Larry tells Stingo that Nathan and Sophie have killed themselves with cyanide. Stingo finds them in Sophie's bed, in each other's arms, wearing the 1930s costumes they once wore for the carefree trip to Coney Island. Alongside them, a book is opened to Emily Dickinson's verse, "Ample make this bed. Make this bed with awe."
As Stingo reads the poem aloud, he's joined by the opera's Narrator. When the young Stingo fades away, the Narrator is left to reminisce about his lost friends. He concludes with the lines, "At Auschwitz, tell me, where was God? The response: Where was man?"
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