The Cold War reached a crisis point in June 1950 when Harry Truman announced that the US would send troops to Korea to battle an invasion of the South by troops from Communist North Korea. Two days after Truman launched the US into the Korean War, the Caltech Board of Trustees moved in private to investigate "whether Dr. Pauling’s services are detrimental to the Institute, and whether his appointment should be terminated."

Then a former Communist Party member and managing editor of the Daily Worker, Louis Budenz, provided the FBI the names of hundreds of people he claimed were concealed Communists. One of them was Linus Pauling. The FBI kept the Budenz list secret while they tracked the named suspects during the summer. The FBI investigation of Pauling uncovered no evidence that he was a Party member -- many others on Budenz’s list were also found not to be Communists -- but the professor’s actions were considered suspicious enough that in October Pauling was given a place on the Security Index, the FBI’s list of America’s highest-profile Communist sympathizers, "fellow travelers" as they were called, all of whom Hoover considered a threat to America. Every one in the Index would be constantly monitored and their files updated every six months.

At the same time, Joe McCarthy, the right-wing Senator, pulled Pauling’s name from the Budenz testimony and publicly denounced him as a security risk who threatened to give away America’s atomic secrets to the Russians. It did not matter much what Pauling said in response. His name had been blackened; he was now inextricably linked in the public mind to those trying to subvert US interests.