In October 1944, Saul Ausländer works as a Sonderkommando Jewish–Hungarian prisoner in Auschwitz. His job is to salvage valuables from the clothing of the dead, drag bodies from the gas chambers and scrub the chambers before the next group arrives to be gassed. He works stoically, seemingly having been numbed by the daily horrors. Among the dead after a gassing, Saul sees a boy who is still barely alive suffocated by a Nazi physician who calls for an autopsy on the boy. Saul steps forth and insists on carrying the body himself to the prison doctor, Miklós, a fellow Hungarian prisoner and a forced assistant to Josef Mengele. He asks Miklós to not cut up the boy, so he can give him a proper Jewish burial. Miklós declines, but says he can have five minutes alone with the boy tonight, before the cremation. Saul goes in search of a Rabbi to perform the funeral ritual. He goes to Rabbi Frankel in the crematorium, who dismisses Saul's concern and suggests that Saul perform the burial himself.
Saul overhears Sonderkommando Abraham, talk about an uprising against the SS-guards with Oberkapo Biederman (Urs Rechn). Biederman first wants to photograph the camp's atrocities using a camera collected from the clothing of an earlier gassed caravan, and smuggle the pictures outside to attract attention and help. Saul asks for another rabbi and Abraham tells him of "the Renegade," a Greek Rabbi who has lost his faith. Saul in return offers his assistance in their plan and is instructed to go with a prisoner (Katz) to repair a shack; he is given a piece of jewellery for use as a bribe in case he's caught. When Saul and Katz arrive at the shack, Saul pretends to fix the front door's lock, while Katz takes out a camera from inside the shack and starts to take pictures of the cremation. Saul hears the guards and hides the camera outside in a drain. The guards search the shack, only to find nothing.
Saul then sneaks onto a truck for another Sonderkommando unit, heading to a nearby riverbank, where the ashes from the crematoria are dumped into the river. Saul finds the Renegade, who refuses to help him. Saul then threatens to alert the Oberkapo of the unit, Mietek, that the Renegade is a rabbi by reciting a Jewish blessing. When the Renegade refuses yet again Saul throws the man's shovel into the water. The rabbi jumps into the river to retrieve the shovel or drown himself. Saul, who can't swim, manages to bring the Renegade back to the riverbank and both are then taken to the SS-commandant of the unit. After an interrogation, the Renegade is executed and Saul is allowed to go back to the unit.
Saul is then confronted by Mietek, who realizes that he is from another unit. To mollify Mietek, Saul gives him the piece of jewellery. Back at the camp, following roll call, Saul sneaks into Miklós's office where he is caught by a group of Nazi officers. One of them pushes Saul around like a puppet and makes a mockery of Jewish dances, finally forcing him out of the room. After searching in vain for the boy's body, Saul confronts Miklós, who assures him that he has hidden it from the other doctors for safety. Saul sneaks into the autopsy room and takes the body back to his own barrack in a sack.
That night Saul is summoned to clean the dinner tables by SS-commandant Moll. Biederman walks in and is ordered to write up a list of seventy names. This leads Biederman to believe that his unit will soon be gassed. Biederman discloses the information to Abraham, who instructs Saul to head to the women's camp, where he will pick up a smuggled package of gunpowder from a prisoner named Ella. When Saul finds himself face to face with Ella, it is clear they know each other. She calls him by name and clasps his hand, but he withdraws. After collecting the package, Saul deliberately falls into a line of newly arrived Hungarian Jews, who are being led into the woods for execution. Saul again looks for a rabbi among the arrivals. A Frenchman named Braun approaches him and convinces Saul that he is a rabbi. Saul disguises Braun as a member of the Sonderkommando and sneaks him into the camp. When Saul arrives at the camp he is confronted by Abraham and realizes that during the turmoil in the woods he has lost the package. On further questioning, he says that the dead boy is his illegitimate son, an assertion Abraham says is not true.
The next morning during roll call, Miklós finds Saul and tells him that he needs a replacement body, similar to the one Saul has taken. The prisoners are then summoned into the crematorium to get back to work, where they discover that Biederman and his unit have been gassed by the SS. Abraham starts a riot with the other prisoners and they attack the SS guards, starting the rebellion. After managing to escape from the crematorium, Saul retrieves the boy's body and escapes to the woods with Braun and few other prisoners. When they reach a river, Saul finds a chance to bury the body, only to discover that Braun is a fraud when he can't recite the Kaddish. When he hears the guards approaching, Saul tries to carry the body across the river. Unable to manage the current with the added weight, he loses his grasp on the sack and is pulled out of the river by Rabbi Frankel as the body floats away. When the prisoners arrive at a shed in the forest, they start to discuss a plan to join the Polish resistance. Saul notices a young peasant boy peeking into the shed and smiles at him, the only time he is shown with a smile. The boy runs away, and makes it a short distance before an SS officer grabs and silences him as guards run past in the direction of the shed. When they have all passed, the officer releases him, and the boy runs into the woods as the sound of gunfire echoes behind him.
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