Guilt
Heisenberg, Bohr, and Margrethe are all wracked by guilt. They cannot escape the idea that they are each responsible for the development of the atomic bomb. They follow endless trains of "what ifs." In the end, guilt is the one sure way to rob yourself of peace. These unfortunate souls find themselves unable to be at peace in their deaths, so here they sit talking. Solely in the hopes of understanding their responsibility in real events, they are methodically running through cause and effect scenarios in order to consider 1941 and the following years from an accurate perspective. Only after looking at the situation from every possible angle do they find peace from their guilt becuase they can accept an appropriate amount of responsibility for their actions and excuse the rest.
Cause and Effect
This entire play is a discussion about the role of cause and effect. Heisenberg and Bohr are running with the idea that causes can always be determined by their effects. It's a pretty tricky business making assumptions about such things. In this text the three protagonists seem to find solace in their convictions about cause and effect. Somehow the detached perpsective of death allows for a new conversation about responsibility. By the end they're all overly eager to blame themselves for the atomic crisis.
Reputation
Both Heisenberg and Bohr appeal to their reputations in order to clear their names. Bohr wants no part in Heisenberg's work in Germany. If he had known how Heisenberg would use his research, he never would have collaborated with him in 1941. Unfortunately those events cannot be changed. Bohr appeals to the commonness of scientists staying with him in order to explain why Heisenberg's visit was insignificant. He had no idea his young pupil would go on to help the Nazis develop atomic capabilities. For his part, Heisenberg insists that he had no choice other than to help Hitler with his atomic program. Heisenberg is known after his death as just that -- the man who almost gave Hitler an atom bomb. Heisenberg sees it differently, however. He believes that Hitler would have inevitably gotten what he wanted, with or without his help. He would have to be a fool to willingly participate if he thought he could've declined, given the devestating effects the work had on his reputation after the war.