Japan, early 20th century. Lieutenant Benjamin Franklin Pinkerton of the American Navy inspects a house overlooking Nagasaki harbor that he is leasing from Goro, a Japanese marriage broker. The house comes complete with three servants and a geisha wife named Cio-Cio-San, known locally as Madama Butterfly. The lease for both the house and the marriage is for 999 years, subject to monthly renewal, which Pinkerton makes certain to clearly articulate. The American consul, Sharpless, arrives breathless from climbing the hill to the house. Pinkerton describes his philosophy of the fearless Yankee roaming the world in search of experience and pleasure. He is not sure whether his feelings for the young girl are love or a whim, but he intends to go through with the marriage ceremony regardless. Sharpless warns him that the girl may view the marriage as something sacred, but Pinkerton brushes off such concerns and they toast with a glass of Whiskey: Sharpless, to Pinkerton's family far away, and Pinkerton to the day that he will have a real, true, American wife.
Butterfly is heard climbing the hill with her friends for the ceremony. In casual conversation after the formal introduction, Butterfly admits her age, 15, and explains that her family was once prominent but lost its position, and she has had to earn her living as a geisha. Her relatives arrive and chatter about the marriage. Cio-Cio-San shows Pinkerton her very few possessions; a fan, pipe, makeup, handkerchief, everything with the exception of a sacred rectangular box- which Goro tells Pinkerton was a gift from the Mikado to her father, with an invitation to end his life, which he accepted.
With this knowledge, Pinkerton returns to the conversation where Butterfly quietly tells him she has been to the Christian mission and will embrace her husband’s western religion. The Imperial Commissioner reads the marriage agreement, and with a signature, pronounces the wedding complete. The relatives congratulate the couple. Suddenly, a threatening voice is heard —it is the Bonze, Butterfly’s uncle, a priest of her former faith. He curses the girl for going to the Christian mission and rejecting her ancestral religion. Pinkerton orders them all to leave and as they go, the Bonze and the shocked relatives denounce and disown Cio-Cio-San. Pinkerton tries to console Butterfly with sweet words. She is helped by Suzuki into her wedding kimono, and joins Pinkerton in the garden, where they spend their first night together as a couple.
Three years have passed since Pinkerton was called away, and Cio-Cio-San awaits her husband’s return. Suzuki prays to the gods for help, but Butterfly berates her for believing in lazy Japanese gods rather than in Pinkerton’s American promise to return one day. She tells Suzuki about her dream of the day that Pinkerton will return: She will see smoke on the horizon, the ship will come into the harbor, Pinkerton will run up the hill, calling "Butterfly," and finally he will enter their house and they will embrace for their grand reunion; which, by articulation, solidifies her faith in her husband even further.
Sharpless appears at the house with a letter from Pinkerton, but before he can read it to Butterfly, Goro arrives with the latest potential second husband for Butterfly; the wealthy and noble Prince Yamadori. Butterfly politely serves the guests tea but insists she is not available for marriage, as her American husband has absolutely not deserted her. She dismisses Goro and Yamadori. Sharpless attempts to read Pinkerton’s letter again and suggests that perhaps Butterfly should seriously reconsider Yamadori’s offer, and softening the blow, asks her what she would do if Pinkerton were never to return. She considers the question seriously, and suggests that perhaps she would return to her life as a geisha, but would rather die.
Outraged by the suggestion that Pinkerton wouldn't return, Butterfly runs into an adjoining room and brings back her proof of Pinkerton's love: their 3 year old son. Butterfly scolds Sharpless for his insensitivity, over the head of the child, saying that his sad mother will have to go and dance for money again in order to survive. She also tells Sharpless that he can tell Pinkerton that the Boy's name is "Dolore" (Sorrow) but on the day of his father's return, his name will be "Gioia" (Joy). Sharpless, too upset to tell her more of the letter’s contents, leaves, promising to tell Pinkerton of the child. Suzuki drags Goro into the house after she hears him suggest that Butterfly does not know who the boy's father is. Butterfly in a rage, threatens to kill Goro, and just when she feels that everyone around her has abandoned hope, a cannon shot is heard in the harbor.
Butterfly and Suzuki take a telescope to the terrace and read the name of the ship that is arriving: U.S.S. Abraham Lincoln; Pinkerton’s ship. Overjoyed and vindicated, Butterfly joins Suzuki in strewing the house with flower petals from the garden until the garden is completely bare. Butterfly asks Suzuki how long she thinks it will take, "One hour?" she asks. Suzuki responds with a knowing "Maybe more..."
Night falls, and Butterfly asks Suzuki to help her put on her wedding kimono, in order to feel as beautiful when she sees him again, as the night that they first met. She remarks at how much three years of crying, and motherhood's stress has made her face seem different. Regardless, she summons strength and excitement enough to make small holes in the paper walls of the shosi so that the three of them; Butterfly, Suzuki, and the child, can keep watch over the harbor for Pinkerton's return. Through the night, the child falls asleep, and so does Suzuki, but Butterfly stays awake and keeps vigil until the sun comes up the following morning.
Dawn breaks, and seeing that Pinkerton has still not arrived, Suzuki insists that Butterfly get some sleep. Butterfly carries the child into another room, singing a lullaby to her son. Sharpless appears at the door with Pinkerton. Suzuki, ecstatic to have been wrong all this time, frantically greets the men, and tries to rush to wake up Butterfly. When the men ask her to wait, she realizes something is wrong, and notices a woman in the garden; an American woman, Kate, who is Pinkerton's new wife. Sharpless asks Suzuki to help them tell Butterfly the painful and earth-shattering news.
Sharpless scolds Pinkerton for his not listening to his advice before the wedding, and Pinkerton is overcome with guilt, knowing the pain he is causing Butterfly, but pauses to reflect on the past days in their little house. Once filled with the sweet aroma of flowers, but now that sweetness turned bitter, and he runs away from the house to not have to face Butterfly. Cio-Cio-San, hearing commotion and what she imagines to be Sharpless, rushes into the main room hoping to find Pinkerton as well, but only sees Suzuki in tears, and Kate instead. Grasping the situation, and understanding that the only reason why Pinkerton has returned was to take the boy back to America with their new family, she agrees to give up the child, but insists Pinkerton return for him. Kate and Butterfly exchange as pleasant a greeting as possible, whereby Butterfly understands that Kate is not at direct fault for her pain. Butterfly says that there must be no happier woman in all the world than Kate, and Kate promises to take good care of the boy.
Dismissing everyone, Butterfly breaks down completely in her solitude, and rushes to unsheathe the dagger with which her father committed Hari-kari, choosing to die with honor rather than live in shame."Con onor Muore chi non puo serbar vita con onore" inscribed on the knife - "Better to die with honor than to live without"
Just as the knife is about to make its final motion, she is interrupted, and the child rushes into the room. Butterfly, temporarily abandoning her suicidal intentions, holds him tightly, and tells him to always remember her face and that his mother loves him; even as he goes far over the ocean and grows up away from her. She says her final goodbye to him, blindfolds him, places an American Flag in his hands, and tells him to "Gioca"- Go Play.
She stabs herself as Pinkerton calls her name, rushing up the hill to find his Butterfly dead, and his little boy, the result of their love, waving the American flag beside her.