Oppenheimer stood against the hydrogen bomb because he believed that it was not necessary to national defense and because he felt that the creation of such a powerful weapon was morally reprehensible. But to some onlookers, Oppenheimer's stance against the Super made it seem that he was being weak on national defense and thus being "soft" on communism. This only gave more ammunition to Oppenheimer's enemies, who were waiting in the wings for their chance remove this suspected communist from the his position of power, once and for all.

In November of 1953, a former government official sent a letter to J. Edgar Hoover, the director of the FBI, alleging that Oppenheimer was a Soviet spy. This letter was all it took to bring the forces of McCarthyism to bear against Oppenheimer. In that age of paranoia and communist witch-hunts, empty allegations were proof to permanently brand someone a communist traitor, and alleged offenders were guilty until proven innocent. Oppenheimer was no exception.

Hoover forwarded the incriminating letter to President Eisenhower, who immediately ordered that Oppenheimer's security clearance be suspended pending an investigation by a three-person Personnel Security Board. It was a trial, though not one that would ever have been allowed under the United States justice system. The hearings were held behind closed doors, and Oppenheimer's defense lawyer had no access to the evidence against the scientist since the data was classified and a matter of national security. Much of the unclassified evidence against Oppenheimer came from unnamed informants and illegal wiretaps, none of which would have been allowed had the trial taken place in a courtroom, rather than behind the closed doors of the security board.

While the investigation was supposedly intended to determine whether Oppenheimer had any communist ties, the secret hearings focused less on his radical past than it did on his behavior during the debate over the Super. This caused many outraged members of the scientific community to speculate that it was for his opinion, rather than for any treasonous acts, that he was being persecuted. Indeed, one of the only prominent scientists to testify against Oppenheimer was Edward Teller, the father of the hydrogen bomb who had been outraged by Oppenheimer's objections to it. The rest of Oppenheimer's fellow physicists, as well as General Groves, eagerly lined up to defend the man who had so brilliantly inspired, motivated, and tended to them through the long Los Alamos years.

However, Oppenheimer's prosecutors did muster some evidence on their side in their claim that Oppenheimer had been less than forthright about his communist past. They focused on an event that took place in 1943, when Oppenheimer had dinner with his old friend from Berkeley, Haakon Chevalier. Apparently Chevalier had attempted to convince Oppenheimer to pass information about the bomb project on to the Soviets. Oppenheimer had immediately refused, but he had also neglected to mention anything about the incident to army intelligence officers. When he finally did tell the military about it, almost a year later, he never mentioned Chevalier's name. While he may have been merely protecting a friend, to the military, it looked as if Oppenheimer had something to hide.

After an exhaustive set of hearings, the Personnel Security Board released its report on May 27, 1954. The Board had voted two to one against Oppenheimer regaining his security clearance. The Board's report of its findings admits that there is no evidence that Oppenheimer was ever a member of the Communist Party, adding that the Board was convinced that Oppenheimer had always remained loyal to his country. Oppenheimer's behavior reflected not disloyalty, but bad judgment. Nevertheless, the report continued, Oppenheimer's behavior in the Chevalier incident, as well as in the debate over the Super and on a number of more minor occasions in between, demonstrated "an arrogance of his own judgement with respect to the loyalty and reliability of other citizens to an extent which has frustrated and at times impeded the workings of the system." The content and findings of the hearings were passed on to the AEC, which, on June 29, 1954, released its own decision, voting four to one against Oppenheimer. According to the AEC's findings, Oppenheimer was to be denied future security clearance due to "the proof of fundamental defects in his 'character.'"