B.F. Pinkerton, a Lieutenant in the U. S. Navy, is inspecting his new house, built on a hillside overlooking Nagasaki harbor. Goro, a marriage broker, has arranged the leasing of the house as well as the marriage of Pinkerton with Cio-Cio-San, a geisha, known as Madame Butterfly. The American consul, Sharpless, arrives for the marriage ceremony and warns Pinkerton that Butterfly may not take the marriage lightly. Pinkerton admits that he does not regard the marriage contract as permanent, but is enchanted with Butterfly. Cio-Cio-San arrives with her friends and tells Pinkerton of her family, confesses that she has renounced her religion for his sake, and displays her few treasured possessions. Her relatives arrive and the marriage ceremony begins. Festivities are interrupted by the girl’s uncle, the priestly Bonze, who curses her for having deserted the religion of her ancestors. The members of the family quickly disperse, leaving Butterfly alone with Pinkerton. He dries her tears and takes her in his arms. As night descends and the stars appear, they sing of their love and slowly enter the house.

Three years have passed and Pinkerton has left Japan, promising to return. Despite the pleadings of her maid, Suzuki, Butterfly has not lost faith in his promise. She is visited by Sharpless and Goro, who try to persuade her to wed the wealthy Prince Yamadori. Butterfly dismisses the suggestion as unworthy of an American wife. Sharpless begins to read a letter from Pinkerton, and when he hints that the lieutenant may never return, Butterfly shows him her son – Pinkerton’s son. The consul does not have the courage to tell her that Pinkerton has married again. He leaves without having finished the reading of the letter. The harbor cannon announces the arrival of a foreign ship. Breathless with excitement, Butterfly recognizes the ship as the Abraham Lincoln, Pinkerton’s ship. She and Suzuki gather flowers and strew them about the house. Then Butterfly dons her wedding gown and takes her position with Suzuki and the little boy to await the arrival of her husband.

Butterfly is still maintaining her vigil as the sun rises. At Suzuki’s insistence, she goes to rest, taking the child with her. Sharpless and Pinkerton enter and Suzuki soon realizes the entire situation. The remorseful Pinkerton learns of Butterfly’s faithfulness and bids an anguished farewell to the scene of his former happiness. As soon as he leaves, Butterfly rushes in. At first mystified by Suzuki’s attitude, she understands all when she sees Kate Pinkerton waiting in the garden. She agrees to give up her child if Pinkerton will return to get him in half an hour. When left alone, she takes up the dagger with which her father committed hara-kiri. Suzuki pushes the little boy into the room in an effort to prevent the suicide, but Butterfly thrusts a toy American flag into his hands, retires behind a screen and stabs herself. She dies just as Pinkerton re-enters to take away his son.