Shmuel does not come to meet Bruno at the fence for the two days after Bruno finds out he will be returning to Berlin soon. On the third day, when Shmuel does appear, he is even sadder than usual. He tells Bruno that his father has disappeared. When Bruno suggests asking his own Father what has happened, Shmuel says he doesn't think that's a good idea because the soldiers hate him and the rest of the people on that side of the fence. He vehemently says that he hates the soldiers, too. When Bruno asks him if he hates Father, too, Shmuel says nothing but wonders how Bruno could be the son of such a hateful person.
Bruno tells Shmuel that he is returning to Berlin. Shmuel is saddened by this news, since he won't have anyone to talk to anymore. Bruno tells him that tomorrow will be the last time they'll see each other, and that he wishes they had gotten a chance to play together. Shmuel suggests that he come over to the other side of the fence, but Bruno reminds him that he would get in trouble. Then Bruno realizes that since he's had his head shaved, he looks a lot more like Shmuel. If Shmuel brings him a pair of striped pajamas, he will be able to sneak over to the other side of the fence secretly and he can help Shmuel search for his father. They make a plan to do it the next day, Friday. Bruno is excited about the chance to have an adventure with his friend and Shmuel is excited that Bruno is going to help him look for his father.
Bruno wakes up on Friday and is disappointed to see that it is raining. Just as Herr Liszt is leaving for the day, the rain begins to let up. Bruno puts on boots and a raincoat and walks through the mud to meet Shmuel at the fence. Shmuel says he had been unsure whether Bruno would come to meet him in the rain, but he has brought with him a pair of dirty-looking striped pajamas. He hands the pajamas under the fence to Bruno, who carefully changes into them, leaving his own clothes in a pile in the mud. The pajamas smell terrible. When Bruno shows Shmuel how he looks, Shmuel thinks to himself that if Bruno were a bit skinnier, it would have been difficult to tell them apart. Bruno tells Shmuel that dressing up in the pajamas reminds him of the plays he used to put on with his Grandmother and Gretel.
Shmuel tells Bruno that he has to remove his boots, too, or he will be recognized. His bare feet sink into the mud; at first this makes him uncomfortable, but then he begins to enjoy the feeling. Shmuel lifts the fence and Bruno shimmies underneath it, becoming quite muddy in the process. Each boy has the urge to hug the other, but neither does. They walk back to the populated part of the camp together and Bruno is surprised at how it looks. He had imagined happy families and children playing games together, shops, a town center, and people chatting.
But in contrast with what Bruno had envisioned, the people are just standing or sitting, "looking horribly sad" (207). They are all too skinny and have shaved heads, which Bruno takes to indicate that they have had lice here, too. Bruno notices that there are two groups of people: the soldiers, who seem to be having a happy time, and the people in the striped pajamas, who are cowering or crying. He tells Shmuel he doesn't like it there and wants to go home, but Shmuel reminds him that he promised he'd help look for his father. Bruno agrees and they spend an hour and a half searching for evidence. They don't find anything, which is what Shmuel had expected, and Bruno says again that he ought to go home.
Just then, the soldiers round up the people around Bruno and Shmuel. Shmuel reassures Bruno that "it happens sometimes... They make people go on marches" (210). Bruno is distressed because he doesn't have time to go on a march - he needs to be home for roast beef dinner. Shmuel tells him not to say anything because the soldiers will get angry, and Bruno obeys. He doesn't understand why all the other people marching with them look so frightened. Just as Bruno is beginning to lose patience and deciding that he really must go home because he is too cold, the group is marched into a warm, airtight room. Bruno apologizes to Shmuel that they weren't able to find his father, then tells him that when he comes to visit him in Berlin, they can spend time with all Bruno's old friends. He makes sure to tell Shmuel that he is his "best friend for life" (213). At that moment, the people in the room with them all gasp as the door is slammed shut and locked. The room becomes dark and chaotic, but Bruno and Shmuel continue to hold hands.
The soldiers search for Bruno for days his clothes and boots are discovered by the fence. Father goes to see them but cannot figure out what happened to his son. Mother and Gretel stay at Out-With for a few months waiting for news of Bruno. One day, Mother has the sudden notion that he might have returned to their home in Berlin, so she rushes back with Gretel but doesn't find Bruno there. Over the next year, Father becomes very disliked by all the soldiers at Out-With. Finally, he returns to the place where his son's clothes had been found and notices the opening in the fence. He realizes what must have happened, and a few months later he is discharged from his post at Out-With and taken away by soldiers.
In Chapter Eighteen, the dramatic irony that has been at work throughout the story takes a tragic turn. The reader does not yet know what the terrible result of Bruno's last adventure will be, but the cliff hanger creates an ironic sense of doom: "[all] in all, it seemed like a very sensible plan and a good way to say goodbye" (199). The boys think this adventure will be their time to say goodbye to each other, when in reality they will be saying goodbye to the world. When the boys get rounded up and forced to march into the gas chamber with the group of Jews, Bruno is worried he won't be home in time for dinner and asks his friend if the marching usually goes on for long. Shmuel answers, "I never see the people after they've gone on a march. But I wouldn't imagine it does" (211). The reader knows that the reason he never sees the people is because they are being marched to their deaths in a gas chamber, but neither Shmuel nor Bruno understands this.
The details of the boys' deaths are omitted, which implies that they represent all the children who died during the Holocaust without completely understanding what was going on. The room they arrive in "felt completely airtight," something that is comforting to Bruno because he has been cold outdoors during the march (212). In fact, the room is airtight because it is a gas chamber. The reader has all doubt removed when the door to the chamber is slammed shut and the people in it gasp loudly. Bruno assumes "it had something to do with keeping the rain out and stopping people from catching colds" (213). When the boys die, they are holding hands, and Boyne doesn't specify whether they ever realize what is happening.
Bruno's limited perspective also comes into play in these last chapters, preventing him from understanding the fate he is about to experience in the gas chamber. As he is marched along with the other prisoners, "he [wants] to whisper to them that everything was all right, that Father was the Commandant, and if this was the kind of thing that he wanted the people to do then it must be all right" (210). Bruno is, of course, completely wrong: this is the sort of thing Father wants the Jews to do, but there is nothing "all right" about it. The very person in whom Bruno has faith is the one who is bringing about the deaths of so many, his own son included.
Shmuel's point of view is inserted into Chapter Eighteen deliberately, to further blur the distinction between the two boys. When Bruno asks him about whether he hates Bruno's Father in addition to all the other soldiers, Shmuel remains silent but thinks to himself about how "he had seen Bruno's father on any number of occasions and couldn't understand how such a man could have a son who was so friendly and kind" (196). The narrator remains in the third person, but reveals insight into Shmuel's thought process in a way which allows us the perspective of someone other than Bruno. When Bruno has put on the pajamas and turns around to show Shmuel what he looks like, "[it] was almost (Shmuel thought) as if they were all exactly the same really" (204). Boyne puts the indication of Shmuel's point of view in parentheses in order to imply that while the thought is Shmuel's, it is also a commentary on the situation generally. Once Bruno puts on the pajamas he looks no different from Shmuel; but really, the distinction made between the Jews and the Germans is arbitrary and erroneous, since they are all human beings.
In the last chapters, Boyne issues a veiled call to action to the reader, who might be living during a time of war or genocide. The most obvious instance is in the ironic tone on the final page of the story, when, after a devastated Father has been taken away from Out-With, the narrator says that "[of] course all this happened a long time ago and nothing like that could ever happen again. Not in this day and age" (216). Boyne means for the reader to consider just the opposite: there are genocides occurring in this day and age, all over the world, and the reader is likely employing various coping strategies to ignore or dismiss them. Bruno's annoyance at being forced to march with the group of Jews in the concentration camp is representative of the disconnect common to many witnesses of genocide. As Bruno is marched through the cold mud and rain, "he longed to be back in his house, watching all this from a distance and not wrapped up in the center of it" (211). This idea is a commentary on the perspective of those who allowed the Holocaust to occur while they remained removed from it, since it did not affect them personally. It applies to all witnesses to genocide in any time or place. The reader is meant to question how easy it is to watch from a distance, as long as one is not victimized.