Sonderkommando were groups of workers (prisoners) who helped dispose of those killed in the camp. They were never directly involved in the killing of other prisoners. The uprising referred to in the mod happened after the camp's resistance group successfully blew up one of the crematoriums. From Wikipedia:
"When the camp resistance warned the Sonderkommando that they were due to be murdered on the morning of October 7, 1944, they attacked the SS and Kapos with axes, knives, and home-made grenades. Three SS men were killed, including one who was pushed alive into a crematorium oven; and some prisoners escaped from the camp for a period. They were recaptured later the same day. Of those who did not die in the uprising itself, 200 were forced to strip, lie face down, and then were shot in the back of the head. A total of 451 Sonderkommandos were killed on this day."
Naturally the mod will take liberties with history, instead turning the player (playing as Auschwitz prisoner Zalmen Gradowski) into a Nazi killing machine. The game's ModDB page calls the first title part of a trilogy of mods about prisoner uprisings in other caps including Warsaw, Poland and Treblinka.