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Bohr watched the Nazis' rise to power with great unease, even as the rest of the world dismissed them as ultimately harmless. In 1933 Hitler became chancellor of Germany, and racial laws barring Jews from public posts were soon announced. Immediately Bohr took action to aid German scientists. On one visit, he met Otto Frisch, who was the nephew of Bohr's colleague, Lise Meitner. Frisch had shown great promise, having published a few important papers at a young age, but he naturally felt anxiety about the threat that the Nazis posed to his career and welfare. Frisch later recalled that Bohr seemed like a kindly father as he smiled and expressed the hope that Frisch would come to work in Copenhagen. That night Frisch wrote to his mother to relieve her own fears, seeing Bohr's intervention as an act of "the good Lord."

Bohr continued to travel through Germany and spread the word that Copenhagen was available as a retreat in case of necessity. Along with his brother and other prominent Danish figures, Bohr helped to form the Danish Committee for the Support of Refugee Intellectuals. He arranged accommodations in his own country while writing to colleagues around the world in search of positions for those who had to flee from the Nazis.

Meanwhile, as Copenhagen became the world center for physics, Bohr had gradually become the symbol of national pride. In 1932 he was invited to occupy "The House of Honor"—set aside semi-officially for Denmark's greatest citizen, the person who brought the greatest honor to the country. The Bohrs moved in and entertained many guests, including the King and Queen of Denmark, Queen Elizabeth and Prince Philip of England, and before any of these, the Rutherfords. But in 1934, tragedy struck the happy household. Bohr was on a sailing trip with his son and two friends when a storm rushed upon them. In the resulting disarray, Christian, Bohr's eldest son, was thrown overboard and lost.

Shaken up by this loss, Bohr moved forward with his research and soon made his next major contributions to physics. 1929 is often considered a turning point in quantum theory: it marked the end of what was called the "heroic period," when the central questions revolved around the workings of the atom. Many scientists even thought that physics was close to finished, and one suggested that, with their job completed, they might turn to biology. But Bohr recognized that no such end was near, and the beginning of the 1930s turned the focus to electromagnetism. One impetus for this shift was a startling discovery by Bothe and Becker, who had found unexpected radiation when directing particles at beryllium. Meanwhile, Rutherford and his chief assistant Chadwick had discovered and named the proton and neutron. These experimental discoveries led to Bohr's brilliant postulation of the compound nucleus. He saw nuclear reactions taking place in two stages. First, a neutron would collide with a proton or neutron, but instead of knocking that particle out, the collision would lead to multiple collisions within the nucleus, thus distributing the original energy among the particles. This excess energy would then have to be released in an action by the system. While this picture of the nucleus seems intuitive today, it was a remarkable advance at the time and took ingenuity to devise. The compound nucleus theory also made possible future insights into nuclear transmutation and disintegration.

Like many previous advances, this one led to consequences that were probably not foreseen—in this case the splitting of the atom and the subsequent development of the nuclear bomb.

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