From late 1951, through his passport difficulties in 1952, and on toward the end of the year -- when he was again denounced as a concealed Communist by overeager informer Louis Budenz -- Pauling maintained an almost invisible political profile. Then came a new president: Dwight Eisenhower, elected in November 1952. Ike seemed even more eager than Truman to root out Communists. A member of his cabinet, Oveta Culp Hobby, Secretary of Health, Education, and Welfare, for instance, began withholding federal research money from suspected Communists. That included Pauling, who was notified in late 1953 that all his research money from the US Public Health Service was being suspended. It amounted to about $60,000 per year. Pauling was advised by a sympathetic USPHS manager to reapply under the names of researchers who worked for him, rather than using his name. It worked. The same grants for the same projects were funded as long as Pauling’s name did not appear. He would not receive another penny from the agency until two years later, when Hobby resigned.

Then, at the end of 1953, another of his passport requests was refused. Pauling’s political silence, it seemed, was gaining him nothing. But he continued to hold his tongue until March 1, 1954, when the US detonated a new type of weapon, a super bomb powerful enough to obliterate an entire Pacific island. The explosive energy of what would come to be called the "H Bomb" surprised even the scientists who designed it. It was strong enough to punch a hole into the upper atmosphere, spewing a cloud of radioactive particles that spread around the globe. The radioactive dust then slowly fell back to earth, creating a new threat that everyone started calling "fallout." Peace activists around the world began organizing to fight further development of the weapon.

Pauling, too, was galvanized by the news. On April 15, he finally broke his long silence and delivered his first talk on bomb policy in two and a half years. He connected it with an impassioned defense of Robert Oppenheimer, who was then being accused of being a Communist sympathizer and threatened with a loss of his security clearance. "Dr. Oppenheimer has been sacrificed by the government," Pauling wrote in a piece that ran in The Nation on May Day, 1954. He urged the United States to mount a concerted political and scientific effort to find "a practical alternative to the madness of atomic barbarism." When a friend complimented him on his Nation piece, Pauling replied, "I have decided that not only is it wrong to permit oneself to be stifled, but it isn’t worthwhile."