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After her honorable samurai father's death, Cho-cho San becomes a geisha at Goro's Tea House to provide an income for her family and get married.  A marriage is almost immediately arranged, when American naval lieutenant B.F. Pinkerton, who was brought to Goro's by his friend, Lieutenant Barton, falls in love with Cho-cho San at first sight and spirits her away into the garden.

Upon finding out that he need only to leave port to divorce her, Pinkerton marries Cho-cho San.  Because her name means butterfly in Japanese, Pinkerton nicknames her "Madame Butterfly."  Their life together is blissful.  She learns American customs but treats Pinkerton deferentially in the Japanese custom, and soon falls deeply in love with him.

Pinkerton promises Cho-cho San that there is room in his heart only for her after she finds a photograph of Adelaide, an American woman, in his trunk.  He is reluctant to tell her, however, of his imminent departure, and she finds out by accident.  Cho-cho San is heartbroken, but cheers up when Pinkerton vows he will be true to her and return in the spring, when the first robin appears.

Three springs pass before Pinkerton returns.  By this time, Cho-cho San's son by Pinkerton is almost three-years-old, and she has refrained from naming him until his father's arrival, affectionately calling him "Trouble."  Despite her family's urging, Cho-cho San refuses to marry again because Pinkerton told her they were married "till death do them part," but her family feels she has dishonored them and disowns her.

In the meantime, Pinkerton has wed Adelaide and returns to Cho-cho San only long enough to tell her of his marriage.  Steadfast, Cho-cho San does not reveal they have a son, although she is devastated by Pinkerton's betrayal and her own sense of shame.  After sending her son to her family accompanied by her servant, Suzuki, Cho-cho San commits hara-kiri.