In 1946, as the FAS scientists labored for peace, the world political situation darkened. In the fall Stalin sealed off the Eastern European nations that Russia had "liberated" during the War, creating what Winston Churchill called an "Iron Curtain" across the continent. At the same time, Chinese Communist rebels grew in power, threatening to take control of the world’s most populous nation. Fears of Communist world domination began to ripple through the United States and the Republican Party quickly took advantage, using strong anti-Communist rhetoric as a club with which to batter the dominant Democrats and their President, Harry Truman. After the 1946 mid-year elections, in which the Republicans gained scores of new congressional seats, the Democrats, too, began shifting their policies toward a hard line with the Communist world. In this changing political scene the liberal scientists’ talk of international cooperation, world government, and free exchange of scientific discoveries with all nations, including those under Communist control, began to sound treasonous to many Americans.

President Harry S. Truman, seeing his political party’s power eroding, decided to take a tougher stance toward Communists both at home and abroad. One result was Executive Order 9835, which established in March 1947 a loyalty and security program prohibiting Federal employees from belonging to or having a "sympathetic association" with any group deemed by the Attorney General to be Communist, Fascist, totalitarian, or in any other way subversive to the interests of the United States. Truman’s "loyalty program," as it became known, started a snowball effect. Individual states started their own loyalty efforts, putting into effect investigations and oaths designed to weed Communists out of the ranks of teachers, administrators, policemen, or any other government employees. This web of national and state loyalty checks would mushroom over the next five years, constituting a extra-judicial system in which government panels could investigate, question, and publicly expose anyone they deemed to be a threat to security. Sometimes the threat was nothing more than attending a meeting of a left-leaning group. The US Attorney General started a list of suspect groups, and as the list grew, the number of Americans with investigatory files in any number of local or national offices, from the state legislature to the FBI, grew as well. Soon the files numbered in the hundreds of thousands. It was the start of a domestic security state.