The setting for Endgame is a bare room with two small windows situated high up on the back wall. This is a shelter for the four characters; the rest of the world is supposed to be dead. The right window looks out over the earth, and the left window looks out over the sea. Hamm is onstage, seated in chair, and covered with a sheet when the play opens. Clov enters and proceeds to set up a ladder so he can look out both windows. Once he has completed this ritual he leaves the room and goes to his kitchen.
Hamm wakes up wanting to play games. He whistles and Clov immediately appears. They discuss Hamm's eyes, which Clov has never looked at. Hamm asks Clov to put the sheet back over him, indicating that he wants to go to sleep. Clov refuses, and Hamm threatens not to feed him anymore. Clov says that then he will die.
Hamm finally asks Clov why he does not leave. Clov indicates that he is trying to leave, and that someday he will. Hamm then wants to know why Clov will not kill him. Their conversation is stunted by the fact that whenever one of them makes a statement, it is countered by the other person. The first speaker then agrees with the counter argument, meaning that the conversation immediately ends.
Hamm's father, Nagg, lifts the cover of his bin and appears, his face white. Hamm immediately curses him, calling him, "Accursed progenitor!" Nagg wants his pap, but instead all he gets is a biscuit to gnaw on. Clov then "bottles" him by pushing him back down into his bin. Hamm wants Clov to sit on top of the bin, but Clov indicates that his legs are so bad that he cannot sit down.
Hamm then comments that nature has forgotten them. Clov argues that there is no more nature. When Hamm points out that they are aging, Clov comments that then nature has not forgotten them. This brief conversation is indicative of their constant wordplay. Hamm then asks if it is time for his pain-killer, but Clov tells him it is not yet time.
After Clov returns to his kitchen, Hamm leans back in his chair and tries to sleep. Nagg emerges again and knocks on Nell's bin. She emerges as well. Nagg asks her for a kiss, but they cannot reach each other because the bins are too far apart. They start to recall past events and remember losing their legs in the famous accident in Ardennes. They then complain that the sand in their bins does not get changed often enough. Nagg offers Nell a bit of the biscuit, but she refuses.
Hamm wakes up and tells them to be quiet. Nell asks if Nagg has anything else to say to her, and when he does not, she tells him she is going to leave him. He asks her to scratch him, but since she cannot reach him, she refuses. He then tries to tell her a joke about a tailor. She recalls the first time he ever told her the joke. Nagg soon starts to tell it.
The joke is about a man who orders a pair of trousers from a tailor. After waiting several days he returns, but they are not yet finished. Every time he goes back to get his trousers, the tailor gives him an excuse about why they are not yet finished. Finally the man explodes in rage and says, "In six days...God made the world...And you are not bloody well capable of making me a pair of trousers in three months!" The tailor replies, "But my dear Sir...look at the world...and look at my trousers!"
Hamm orders Nagg to be silent and whistles for Clov. He orders Clov to chuck the two bins into the sea. Clov goes over to Nell and feels her pulse, and after she utters the final word, "desert," he pushes he back into the bin. He then tells Hamm that Nell has no pulse. Hamm, after making sure both Nagg and Nell are back in their bins, asks for his pain-killer again. Again, Clov refuses to give it too him, saying it is too early.
Clov then pushes Hamm's chair around the room in a circular fashion. Hamm says, "Right round the world!" and wants Clov to "Hug the walls." Clov finally pushes the chair up against the wall and Hamm knocks on it. After declaring that the bricks are hollow, Hamm demands to be put back in his spot. He carefully, and comically, forces Clov to put his chair in the dead center of the stage.
Hamm then wants to know about the weather. He makes Clov get the ladder and look at the earth. Clov says he sees "Zero...zero...and zero." Hamm then demands that Clov look at the ocean. The only thing Clov sees is that sun has gone down and that it is gray outside.
Clov suddenly realizes that he has a flea. Hamm says, "But humanity might start from there all over again! Catch him, for the love of God!" Clov gets some flea powder and pours it down his pants until he is sure that he killed the flea. Hamm then decides that he wants to leave the shelter. He orders Clov to build him a raft so he can leave "tomorrow." He then asks for his pain-killer again, but again Clov refuses to give it to him.
Clov discusses leaving Hamm again, but as before he is not ready to go. Hamm reveals that he, "was a father to [Clov]." This comment makes their relationship unclear; is Clov a servant or Hamm's son? Hamm then demands his dog, which turns out to be a toy dog that is missing a leg. Hamm makes Clov hold the dog in a begging position so that he can pet him. He then orders Clov to get his gaff. Clov comments, "Do this, do that, and I do it. I never refuse. Why?"
Hamm takes the gaff and tries to push himself with it, but he soon gives up. Hamm relates a story of a madman who used to look at the world and only see ashes. He then asks Clov how he will know the difference between Clov leaving him or Clov dying in the kitchen. Clov indicates that if he dies, the place will stink. Hamm then points out that the place stinks already.
Hamm orders Clov to think of a solution. Clov decides to set the alarm clock as a sign that he has left. If Hamm hears the alarm, he will know that Clov is gone, whereas if there is no alarm, then Clov is dead. He quickly tests the alarm to make sure it is working. Hamm asks for his pain-killer, but Clov will not give it to him.
Hamm then says that it is time for his daily story. This is a semi-biographical story that Hamm invents a part of every day. Clov wakes up Nagg and Hamm bribes his father into listening to the story. The story consists of Hamm, a prosperous man with money and food, watching a man crawl towards him on his belly. The man petitions Hamm to save his little boy. He explains that everyone is dead in his hometown except for his little boy, whom he wants Hamm to save before the boy starves to death. Hamm gets extremely angry with the man for asking for food, but when he calms down he offers the man a job. The man accepts and then begs to have his child with him. Hamm ends the story at that spot.
Clov returns from the kitchen and informs Hamm that there is a rat in the kitchen. He has tried to kill it, but without success. Nagg then demands his sugar-plum, which is what Hamm promised him if he would listen to the story. Hamm insists that they pray first. After some silent prayer, Hamm comments, "The bastard! He doesn't exist!" Hamm then tells Nagg that there are no more sugar-plums. Nagg comments that having such an ungrateful son is "natural" given that he used to ignore Hamm's cries when Hamm called for him as a child. Nagg then knock on Nell's bin, but when she does not appear he disappears back into his own bin.
Hamm tries to touch the toy dog again, but is has fallen to the ground. Clov picks it up and gives it to Hamm before starting to clean up the floor. Hamm orders him to stop cleaning up and makes Clov drop all the things back onto the floor. Hamm then recounts the story he told to Nagg; Clov compliments him being able to continue the story.
Hamm has Clov check on Nagg and Nell. Clov says that it appears as if Nell is dead, whereas Nagg is merely crying in his bin. Wanting some light, Hamm has Clov push his chair to one of the windows. He does not feel any light and orders Clov to move him to the other window, the window that looks out towards the sea. Hamm finally gives up when Clov tells him there is no light.
Hamm then calls to Nagg. Clov goes over and speaks to Nagg, who refuses to come out of his bin. Clov soon leaves, and Hamm delivers a long soliloquy. He remarks that when he ends his story, he might start another one. At the end of his soliloquy he whistles for Clov, and is surprised when Clov appears with the alarm clock.
Clov indicates that he has not left yet. Hamm then asks for his pain-killer and is excited to learn that it is the right time for it. However, Clov cruelly tells him that there is no more pain-killer. Hamm is crushed to learn that he will have to suffer without any pain-killer, and in the meantime Clov hangs up the alarm clock.
Hamm then orders Clov to look at the earth again. Clov dutifully climbs the ladder, but accidentally looks out of the left window and sees the ocean. He first thinks that the land is under water before realizing that he is at that wrong window. He goes over to the other window and climbs up, but Hamm requires that he use the telescope. Clov climbs back down the ladder and searches for the telescope.
While Clov is searching, Hamm demands his dog. Clov angrily takes the dog and hits Hamm on the head with it before handing it to him. Clov finally finds the telescope and climbs the ladder with it. He looks around and surprisingly spots a small boy. Clov immediately picks up the gaff with the intention of killing the boy, but Hamm stops him. Clov is surprised, and asks, "No? A potential procreator?," indicating that the boy is a threat because he might reproduce.
Hamm tells Clov, "It's the end, Clov, we've come to the end. I don't need you any more." He then makes Clov leave the gaff. Clov hands Hamm the gaff and places the alarm clock on Nagg's bin. Hamm begs him to say something before leaving, and Clov eventually starts a speech that Hamm quickly cuts off.
Hamm then asks Clov for a last favor, but Clov has already left the room. Hamm starts to talk to himself, and while he speaks Clov silently returns, dressed for all weathers. Hamm continues to speak, and he soon whistles for Clov, who still does not move. Hamm then throws away the dog and tosses the whistle to the audience. His last act is to cover his face with his handkerchief and sit motionless on his chair.