After Germany surrendered on May 7, 1945, the British interned Heisenberg and other German nuclear physicists for questioning. Heisenberg and all concerned were under the impression that their research was ahead of the Americans'. The Germans were, therefore, shocked and embarrassed when news arrived of the American bombing of Japan. In reality, their resources did not compare with those of the Manhattan Project, and they did not want to ask for more aid, since they sincerely believed that the bomb would not be completed before the war's end–no nation would want to spend valuable resources on an indefinite project. Some of the German scientists asserted that they had never wanted to complete the bomb because they feared what Hitler would do with it; instead, they concentrated on building a reactor for more constructive purposes. Such an account, however, seems questionable at best.

When Heisenberg returned to Germany in 1946, his goal was to rebuild the state of German physics. In doing so, he spent much of his energy not on research but on science policy. For example, he took an active role in the establishment of the Centre Européen pour la Recherche Nucléaire (CERN) in Geneva, with the hope that it would rival American facilities. Heisenberg was also appointed president of the Alexander von Humboldt Foundation to lure foreign post-doctorates to Germany and thereby reestablish its international contacts. In 1958, he finally returned to Munich as director of the Max Planck Institute of Physics.

Heisenberg's next and perhaps last major contribution to physics did not come until the late 1950s, when he began work with Pauli on a new unified field theory of elementary particles. However, just before publication, Pauli withdrew his support and criticized the equation as incomplete and insufficient. Since then, the formula has been refined, and maintains a significant place in the history of physics.

After Heisenberg's move to Munich, his career was approaching its end. He would continue to lecture and travel for the next seventeen years, but instead of focusing on new research, his main goal was to establish his place in the intellectual tradition of his science. In the early 1970s, he was diagnosed with advanced cancer of the kidneys and gall bladder, and little could be done to treat it. His condition worsened in 1975, and he passed away peacefully on February 1, 1976, in his home in Munich.

The legacy Heisenberg has left is unclear. In helping to establish quantum mechanics and in formulating the uncertainty principle, he had two of the most important contributions to twentieth-century physics. In retrospect, history might not be able to forgive his compliance with the Nazis, but one should at least avoid oversimplifying his dilemma. Heisenberg felt bound to his culture and people and wanted to be in Germany to reconstruct the nation when the Nazi regime passed, as he believed it inevitably would. He felt that Germany needed him, and it was this sense of duty that kept him there. Whether or not we agree with Heisenberg's choice, it was not made in fear or passivity, but a commitment to the values that he considered most important.