The setting is a bare interior with gray lighting. There are two small windows with drawn curtains, a door, and two ashbins covered by an old sheet. Hamm sits on an armchair with wheels, covered by an old sheet. Clov stares at Hamm, motionless. Clov staggers off-stage and returns with a stepladder and draws open the curtains for both windows. He removes the sheet from the ashbins and raises the lid of both and looks within. He removes Hamm's sheet. Hamm, in his dressing-gown, a whistle hanging around his neck, and a handkerchief over his face, appears to be asleep. Clov says, "It's finished." He says he'll go to his kitchen and wait for Hamm to whistle him. He leaves, then comes back, takes the ladders and carries it out. Hamm awakens and removes the handkerchief. He wears dark glasses.

Hamm folds away his handkerchief. He questions whether anyone suffers as much as he does. He says "it's time it ended," but he "hesitate[s]" to end. He whistles and Clov enters. Hamm insults him and orders Clov to prepare him for bed. He asks what time it is, and Clov replies "Same as usual." Hamm asks if he has looked out the window, and Clov gives his report: "Zero." Hamm commands him to get him ready, but Clov doesn't move. Hamm threatens to hold back food from him, and Clov goes for Hamm's sheet. Hamm stops him and asks why Clov stays with him; Clov asks why Hamm keeps him. For Hamm, there's no one else; for Clov, nowhere else. Hamm accuses Clov of leaving him—Clov concedes that he's trying to do so—and that Clov doesn't love him. He asks why Clov doesn't kill him; Clov replies that he doesn't know the combination of the larder. From one of the ashbins, Nagg emerges in a nightcap. Nagg cries for his pap, but since there's none left, Hamm whistles for Clov to get a biscuit. Nagg complains, and Hamm directs Clov to close the lid on him. Clov says there's no more nature, and Hamm refutes this, arguing that their bodies and minds change. After some more debate, Hamm asks him what he does in his kitchen. Clov says he looks at the wall and sees his light dying.

Nagg emerges from his bin, biscuit in mouth, and listens. Hamm tells Clov to leave, which Clov says he's "trying" to do and then does. Nagg knocks on the other bin, and Nell emerges. Nagg asks her to kiss him; they try but cannot reach, and Nell asks why they go through the "farce" every day. Their sight (and Nell's hearing) is failing. Hamm tells them to quiet down, and thinks about what he would dream of if only he could sleep. Nell rebukes Nagg for laughing at Hamm's misery. Nagg tells her a story about a tailor that has often made her laugh, especially the first time he told it to the day after they'd gotten engaged: a tailor keeps botching and delaying a customer's orders for trousers until the customer explodes and points out that God created the world in six days, while the tailor has taken three months for the trousers. The tailor tells him to compare the world with his beautiful trousers. Hamm calls for silence. Nagg disappears, and Hamm whistles for Clov and tells him to throw the bins into the sea. Clov checks Nell's pulse and says she has none. They discuss Hamm's painkiller medicine and Hamm's deceased former doctor. Hamm asks Clov to move him around on his chair and, as he can't see for himself, to hug the walls. Hamm directs Clov to return him back to his spot in the exact center.

Hamm tells Clov to check outside with the telescope. Clov's report is "Zero." Clov asks why they go through the farce everyday, and Hamm answers that it is routine. Hamm wonders if he and Clov are beginning to "mean something"; Clov scoffs at this notion. Clov scratches a flea on his body. Hamm is astounded that there are still fleas, and begs Clov to kill it, as "humanity might start from there all over again!" Clov gets some insecticide and sprinkles it inside his pants. Hamm proposes that he and Clov leave for the South. Clov declines, and Hamm says he'll do it alone and tells Clov to build a raft. Clov says he'll start, but Hamm stops him and asks if it's time for his painkiller—it's not—and inquires about Clov's ailing body. Hamm asks why Clov doesn't "finish" them, but Clov says he couldn't do it, and will leave. Hamm asks him if he remembers when he came here, but Clov says he was too small. Hamm asks if Clov remembers his father—he doesn't—and says that he was a father to Clov.

Before Clov can leave, Hamm asks Clov if his dog is ready. Clov returns with a three-legged toy dog, which he gives to Hamm. Hamm tells Clov to get him his gaff, and Clov wonders out loud why he never refuses his orders. He gets it for Hamm, who unsuccessfully tries to move his chair around with it. Hamm recollects a madman painter-engraver friend of his who thought the end of the world had come, seeing ashes instead of nature. Hamm asks how he'll know if Clov has left. Clov decides he'll set an alarm clock, and if it doesn't ring, it means he's dead. Hamm says it's time for his story, but Clov doesn't want to hear it. Hamm tells him to wake his father, and Clov looks into the ashbin of the sleeping Nagg.

Clov reports that Nagg doesn't want to hear Hamm's story, and wants a sugarplum if he must listen. Hamm agrees, and Clov leaves. Hamm asks Nagg why he produced him, and Nagg says he didn't know that it would be Hamm. Hamm tells a story about how a beggarly man came crawling to him on Christmas Eve. The man revealed he had left behind a small boy in his distant home, alone, and wanted food for the boy. Hamm says he took the man into his service, and was asked if he would take the child, if he were still alive. Clov comes in and reports that there's a rat in the kitchen, and that he's exterminated half of it. Hamm says he'll finish it later, but now they'll pray to God in silence. They are all disappointed by the lack of a godly response, and Hamm believes God doesn't exist. Nagg remembers how Hamm would call him when he was scared as a child, and not his mother. He didn't listen to him, he says, but he hopes the day will come again when Hamm will depend on his father. He knocks on Nell's lid, but with no response he retreats into his bin and closes the lid.

Hamm gropes for his dog. Clov hands it to Hamm, who soon after throws it away. Clov cleans up the room, as he loves order, but Hamm makes him stop. Before Clov can leave, Hamm tells him to stay and listen to his story; he repeats the last bit, and says he's too tired to finish it, or to make up another story. He tells Clov to see if Nell is dead; he looks into the bin and says it looks that way. Nagg hasn't died, but he's crying. Hamm asks Clov to push his chair under the window, as he wants to feel the light on his face. He says he feels sunshine, but Clov says it isn't really the sun. Clov pushes Hamm back to the center. Hamm twice calls for his father, and tells Clov to see if Nagg heard him. Clov investigates and says Nagg isn't crying anymore, but sucking his biscuit. Hamm asks Clov to kiss him on the forehead, or hold his hand, but Clov refuses. Hamm asks for his dog, and then rejects the idea, and Clov leaves, vowing that either he'll kill the rat or it'll die.

Alone, Hamm takes out his handkerchief and spreads it before him. He considers finishing his story and starting another, or throwing himself on the floor, but he isn't able to push himself off his seat. He ruminates on his eventual death, and then whistles. Clov enters with the alarm clock. He reports that the rat got away from him. Clov says it's time for Hamm's painkiller, which relieves him until Clov reveals there's none left. Hamm tells him to look at the earth. Clov reminds him that after Mother Pegg asked Hamm for oil for her lamp, and he refused her, she died of darkness. Hamm feebly says he didn't have enough, but Clov refutes this. Clov wonders why he obeys Hamm, and Hamm answers that perhaps it's compassion.

Clov finds the telescope. Hamm asks to be put in his coffin, but Clov says there is none left. Clov takes the telescope, goes up the stepladder, and sees a small boy out the window. He says he'll investigate with the gaff (a hook-like tool), presumably to kill off the "potential procreator," but Hamm says the boy will either die outside or come inside. He tells Clov that they've come to the end and he doesn't need him anymore, and asks him to leave him the gaff. Before Clov leaves, Hamm asks him to say something "from your heart." Clov repeats a few things "They said to me," and reflects on the pain of life.

Hamm stops him before he leaves and thanks him for his services. Clov thanks him, and Hamm says that they are obliged to each other. He asks him to cover him with the sheet, but Clov has already left. He tries to move the chair with the gaff. Clov enters, outfitted for his journey. Hamm doesn't know he's there, and throws away the useless gaff. He resumes telling his story about the man and his child, repeating how the man wanted his child with him. Hamm recalls it was the moment he was waiting for. Hamm twice calls out "Father" and, not hearing anything, says, "We're coming." He discards his dog and his whistle. He calls out for Clov, but hears nothing. He takes out his handkerchief, unfolds it, and says "You…remain." He covers his face with the handkerchief and sits motionless.