Japan,1904. Pinkerton, a U.S. Naval officer, rents a house overlooking Nagasaki harbor. The house is for him and his geisha wife named Cio-Cio-San, known as Madame Butterfly. Pinkerton intends to marry Madame Butterfly, although he is not sure of his feeling for the young girl. However, he says that one day he will take a proper, American wife. The wedding is to take place at the house. Madam Butterfly tells Pinkerton that she has been to the Christian mission and has converted to Christianity because of him. After the wedding ceremony, the relatives of Butterfly congratulate the couple. Suddenly her uninvited uncle appears and curses her for converting to Christianity and rejecting her ancestral religion. The shocked relatives denounce Madam Butterfly. Pinkerton orders them to leave. Pinkerton and Butterfly sing a love duet and make love in the garden.
Three years later, Butterfly is still waiting for her husband’s return, as he had left shortly after their wedding. Her maid, Suzuki, prays to the gods for help, but Butterfly berates her, as she is sure that Pinkerton would return. The American Consul, Sharpless, comes to the house with a letter from Pinkerton. Before he can read it, Goro, the marriage broker who arranged Madame Butterfly’s marriage, appears. Goro is trying to marry her off again, and brings the latest potential husband, the rich Prince Yamadori. Butterfly insists that she is not available for marriage, as her American husband has not deserted her. Sharpless thinks that perhaps she should reconsider Goro’s offer. Then Madame Butterfly shows the consul her small child. Sharpless is too upset to reveal to her what is in the letter and promises her to tell Pinkerton of the child.
A cannon shot announces the arrival of a ship in the harbor. Butterfly and Suzuki take a telescope and see that it is Pinkerton's ship. Overjoyed, Butterfly and Suzuki prepare for his arrival, and then they wait.
Dawn breaks and Butterfly finally falls asleep. Sharpless, Pinkerton and Kate, Pinkerton’s American wife, arrive at the house. As Pinkerton sees how Butterfly has decorated the house for his return, he is overcome with guilt. As he cannot face her, he runs from the scene leaving Suzuki, Sharpless, and Kate to break the news to Butterfly. Hoping to see Pinkerton, Butterfly rushes but sees Kate instead. Realizing who the American woman is, Butterfly dismisses everyone, prays to statues of her ancestral gods, says goodbye to her son, and blindfolds him. She takes the dagger, with which her father committed suicide, and stabs herself. Pinkerton rushes in, calling her name. He is too late.