Gerstein is the riveting, true story of Kurt Gerstein, an eccentric youth minister whose devotional literature sold to tens of thousands throughout pre-Nazi Germany. With the National Socialist takeover in 1933, Gerstein finds himself on an almost immediate path of defiance against the Nazis, twice imprisoned for anti-Nazi protests. Upon his third imprisonment, he feels called by God to join the elite SS troops and become, as he puts it, "God's Spy"-a moniker S ren Kierkegaard gave himself a century earlier.

Gerstein enters SS training and passes. Although Gerstein does not realize it at first, given his background and education as a mining engineer, the SS leaders see in him one who can serve the National Socialist cause. Subsequently, he is asked by an SS commander how one would most effectively transfer poisonous gases into an enclosed room. Hesitating at first, he is prodded to respond. He later finds out that his answer solved an early mechanical problem in what the Nazis would carry out as their "Final Solution" against Jews.

In the years that follow, Gerstein creates sabotage efforts to thwart the extermination of Jews, writing in his journals much of what he saw. He must keep all the details of his work as "God's Spy" from his wife for fear that she would be interrogated for information. He eventually, but unsuccessfully, warns the British and American embassies of what is taking place in the death camps. He even expresses alarm to a Vatican official, but to no avail. No one believes his tales of horror. His journals will not be read until the Nuremberg Trials after the war.

On June 6, 1950, the basic facts of Gerstein's reports are verified before the land court of Darmstadt in Germany. On August 17, 1950, Gerstein is declared a Nazi offender by a denazification court. Gerstein's wife, with the help of Baron von Otter and other significant friends, obtain a pardon for her husband by the Premier of Baden-Württemberg on January 20, 1955.