As the sun rises, Suzuki awakens and expresses her disappointment that Pinkerton has not arrived. Butterfly remains sure that he will return, and takes her son to the bedroom to sleep, where she also falls asleep. Suzuki stays in the front room and waits, when suddenly there is a knock at the door.
Pinkerton and Sharpless are there. Pinkerton instructs Suzuki to let Butterfly sleep and wonders how she knew that he was coming. Suzuki tells him that Butterfly has remained aware of every ship that enters the harbor for the last three years, so that she could be ready when he arrived. Sharpless scolds Pinkerton, telling him that he knew that Butterfly would react this way.
When Suzuki spots a woman in the garden, Sharpless tells her that it is Pinkerton's wife, and Suzuki is shocked. While Pinkerton looks around, Sharpless consults with Suzuki, and suggests that they must try and help Butterfly's son, even though they cannot save Butterfly. He tells Suzuki that Kate, Pinkerton's wife, wants to take care of the child, and Suzuki goes to meet Kate.
Left alone with Pinkerton, Sharpless tells his friend that he has made a mistake in how he has handled Butterfly. Pinkerton admits that he was wrong to marry her, but then asks Sharpless to tell Butterfly the news. He then sings an aria about how regretful he is about what he has done. In the course of it, he suggests that he will always be haunted by Butterfly. As he finishes the aria, he leaves, just as Suzuki and Kate come inside.
Kate tells Suzuki to tell Butterfly that she will take care of her child with great care and affection. Suzuki promises that she will tell Butterfly, but insists that she must do it alone. They are soon interrupted by Butterfly, who awakens and calls for Suzuki from the bedroom. While Suzuki tells her to stay in her room, Butterfly enters and is confused to find Suzuki crying. Suddenly, she sees Sharpless and Kate in the garden, and asks Suzuki if Pinkerton is still alive. When Suzuki confirms that he is, Butterfly finally realizes that he is not returning. When Sharpless identifies Kate as "the unwitting cause of your misfortune," Butterfly then puts it together that Kate is Pinkerton's wife.
Kate comes over and apologizes to Butterfly, as Sharpless suggests that her son should come with them. Butterfly calls Kate "the happiest woman in the world" and responds that she will only give up her son if Pinkerton is there. She tells Kate and Sharpless to deliver a message to Pinkerton to come back in half an hour. When they leave, she dissolves into weeping. She orders Suzuki to close up the windows and keep the spring light out, then tells her to go in the other room with her son while he plays.
Alone, Butterfly kneels in front of the Buddha statue and prays to her ancestors. After doing so, she grabs her father's knife, reading the inscription, which says, "Let him die with honor who cannot live with honor."
Butterfly's son comes into the room, and she tells him to not become sad when she leaves him, but to remember her face. She also tells him that he is a gift, before tying a blindfold around his eyes, and handing him an American flag to wave upon the arrival of Pinkerton.
Butterfly goes behind the screen and commits ritual suicide. As Pinkerton arrives, he calls to Butterfly, but she is already dead.
Pinkerton returns to a house that is completely frozen in time. In her devotion to her American husband, Suzuki has kept every element of the house the same, and when she sees that he is coming, she fills the rooms with flowers to remind him of their wedding day. He is shocked to find that his momentary affair with Butterfly has left her suspended in time, dreaming of his return. While it was only a brief fling for him, she thought that their love was forever, and has deluded herself into believing that she can maintain the world of the past.
Pinkerton's ignorance about the pain he was causing Butterfly is made all the more devastating when it is revealed that he has brought his American wife, Kate, to the house. Not only must Butterfly suffer the indignity of being abandoned by the man who promised to be her husband, but she must also learn that he has married an American woman in her place. All of this is heightened by the fact that Butterfly falls asleep before Pinkerton arrives, creating dramatic irony in which we know that Pinkerton has betrayed her, but she has no idea.
Yet another indignity committed against Butterfly, again without her knowledge, is the arrangement to have her child with Pinkerton go and live with Pinkerton and Kate. Sharpless rationalizes that, even if they cannot save Butterfly from her fate, they can at least save her son by giving him a chance at a life in America. Because the narrative centers Butterfly as the protagonist, the audience empathizes with her plight, and the fact that she will not only be separated from her husband, but from her child as well.
Pinkerton's betrayal is enough to jolt Butterfly out of her delusions of both Pinkerton's loyalty and her own American-ness. As soon as Kate and Sharpless have left the house, she bows before a statue of the Buddha and prays to her ancestors. Without the devotion of Pinkerton, Butterfly holds no illusions that she is a Christian American wife, and remembers her spiritual past. It is almost as if Pinkerton was some kind of curse, keeping her alienated from her true self, locked in a dynamic in which she had no self-knowledge, and as soon as he is truly gone, she is ready to know herself again.
After all of her delusion and tragedy, Butterfly's only redemption is the promise of dying with honor. Returned to reality, after having been so grossly betrayed by Pinkerton, with all his empty promises and negligence, Butterfly decides that the only dignity to be had is in committing ritual suicide. Indeed, the inscription on the dagger with which she kills herself reflects her philosophy in this moment: "Let him die with honor who cannot live with honor." Deprived of the honor she was promised in marriage, Butterfly must try to find it in taking control of her own destiny.