Werner Heisenberg lived through two World Wars, in the losing country both times and on the decidedly morally objectionable side the second time. The questions will always surround his career: why did he remain in Germany, and why did he choose physics over ethics?
The aftermath of World War I meant economic and political instability in Germany. Fear of communism left the nation in a state of paranoia. Rising inflation put all families in distress. Heisenberg himself was sent to a farm for one summer where he experienced hard labor for the first time. Political instability and general disillusionment also drove him to the youth movement, retreating along with many of Germany's young people. The activities of this youth movement taught Heisenberg to question tradition, a skill that would prove invaluable for his scientific career.
Despite the disrupting influence of the war, Heisenberg managed to achieve a world-class education, perhaps largely due to independent study. This education prepared him for a sizable role in what many view as the golden years of physics. Max Planck and Albert Einstein began the revolution with quantum theory. Einstein also changed the world with his theory of relativity, altering such time-honored principles as gravity and the absolute nature of space and time. Further along, Ernest Rutherford and Niels Bohr offered increasingly detailed pictures of the atom, and Heisenberg's peer Wolfgang Pauli added his own insights. Several such contributions from Pauli and others paved the way for Heisenberg's first major contribution–the establishment of a matrix-based quantum mechanics. After this, Heisenberg continued to lead the way in many searches, including the pursuit of a way to unite relativity and quantum theory, which continues to this day.
While the physics community was thriving, Germany was not making the situation easy for its scientists. One by one, many of Heisenberg's most celebrated colleagues were resigning–whether voluntarily or because they were forced–and leaving the country. Non-Jewish scientists were leaving as well, whether in protest or in fear of worsening conditions in Germany. Moreover, Nazi propagandists were attempting to discredit Einstein's relativity as "Jewish physics" and saw Heisenberg–who defended the work, if not explicitly the man–as carrying the "Jewish spirit." The crusade, led by Nobel Prize-winning experimentalists whose work had become obsolete, turned against theory itself, undermining everything for which Heisenberg had worked.
It was at this point that Heisenberg had to make his crucial decision of whether to stay or go, and he chose to remain in Germany. Perhaps the only explanation is that he could not leave the culture and people he cherished, and that he truly believed that the situation would change for the better (it did with Germany's defeat, but it took much longer than he probably expected). Heisenberg wanted to remain for the rebuilding of German science and culture, and in the meantime he would have to comply just enough to avoid damaging his reputation. On the other hand, we might question Heisenberg's emphasis on saving German physics, because his attempts to maintain Germany's stature could be viewed as an implicit acceptance of the legitimacy of the Third Reich's and Nazism. That a public resignation or outspoken criticism would have affected the political situation was unlikely, but history cannot overlook Heisenberg's willingness to cooperate with the regime despite apparent personal indignation.
Heisenberg believed for his entire life that science and politics should not mix. The most obvious opponent of this stance was Albert Einstein, who as a Jew not only broke ties with Germany, but also actively used his international fame to raise support against it. Heisenberg lived to see the end of the Nazis, but he could not avoid the recognition that American physics had surpassed his own country's science. The Americans had built the atomic bomb, while Heisenberg and the Germans not only failed but also had been convinced that the possibility was remote at best. Nevertheless, Heisenberg got his wish: in the aftermath of the war, he was there to rebuild his culture and the science that had been such an essential part of it.