Cook agreed and he later recalled that he changed his mind on the case after he examined the testimony of Whittaker Chambers. He later recalled: "Well, here was a guy who committed perjury so many times - admittedly so. I didn't see how anybody could trust anything he said. The typing process as he described it didn't make sense. Why would the Hisses spend all that time typing the documents when they supposedly had a whole system set up to photograph them? It was like that with the whole damn thing. When you looked at the government's case, it didn't make any sense down the line, anywhere. One after another as the arguments against Hiss fell apart, I realized I had been brainwashed by my own profession. Until then, I thought that if the story against him was generally accepted, then it had to be true. I should have known better, but I didn't."

Cook's article on Alger Hiss was published in Nation Magazine on 21st September, 1957. He argued that Hiss was a victim of McCarthyism and was not guilty of the accusations made by Whittaker Chambers who had accused Hiss of being a Soviet spy while working for the State Department. Hiss later commented: "It was the times. There was this great wave of hysteria about the great Russian communist menace, and I think the jury was susceptible to that. A lot of average people were. When you have an hysteria like that built in and bastards like Joe McCarthy are beating the drums, it affects the average person. They figure when there's smoke, there has to be fire."

Cook's book on the case, The Unfinished Story of Alger Hiss, appeared in 1958. According to Cook this resulted in him being investigated by the Federal Bureau of Investigation. Cook's next book, The Warfare State (1959), was about the Military Industrial Congress Complex. This was followed by What Manner of Men: Forgotten Heroes of the Revolution (1959) and a biography of Theodore Roosevelt entitled, Rallying a Free People: Theodore Roosevelt (1961).

Cook was unconvinced that John F. Kennedy had been assassinated by a lone-gunman, Lee Harvey Oswald. He wanted to investigate the case at the scene of the crime in Dallas but Carey McWilliams was unwilling to fund the trip. Cook did carry out research on the Mannlicher Carcano, the alleged murder weapon, and came to the conclusion that no assassin would have used such a "grossly inferior rifle". However, "Carey McWilliams was not enthusiastic about the trend of my researches".

Fred J. Cook's next book The FBI Nobody Knows (1964) was highly critical of the J. Edgar Hoover and the Federal Bureau of Investigation. This was followed by a book on Barry Goldwater that was entitled, Barry Goldwater: Extremist of the Right (1964). After the book was published it was attacked by Billy James Hargis on his daily Christian Crusade radio broadcast, on WGCB. Cook sued, arguing that under the FCC's Fairness Doctrine he was entitled to free air time to respond to the attack. This was eventually upheld by a ruling of the Supreme Court.

In 1965 Rex Stout published the novel, The Doorbell Rang. The novel concerns the publication of Cook's book, The FBI Nobody Knows. In the novel, the wealthy Mrs. Rachel Bruner buys 10,000 copies of Cook's book and sends them to persons of influence, including cabinet members, Supreme Court justices, members of Congress and heads of corporations. Bruner believes that as a result of her actions she is being persecuted by the FBI and employs Nero Wolfe to investigate the organization.

After the publication of the Warren Commission Cook decided he must write an article on the Kennedy assassination. Warren Hinckle, the editor of Ramparts Magazine, agreed to publish the 20,000 word article. It was delivered in September, 1965, and was due to appear in its December issue. However, at the last moment it was pulled. He was told it would be in the January 1966 issue. Once again Hinckle failed to keep his promise and in March he told Cook that he had decided not to publish the article. Cook told Ray Marcus that it was "the worst double-cross I have had from a publisher". In April, 1966, Cook received a "token payment" of $500, along with his unpublished manuscript.

Cook now returned to Carey McWilliams and asked him to publish it in the Nation Magazine. Again he refused but when Cook told him that Edward Jay Epstein was about to publish Inquest: The Warren Commission and the Establishment of Truth, it might help him to get in before him. McWilliams saw the logic of the argument and the two-part article was published in June, 1966. Both parts of the article appeared with editorial disclaimers.

The first part, published on 13th June, was entitled Some Unanswered Questions and concerned itself with the way the Warren Commission Report dealt with the events in Dealey Plaza. Cook pointed out: "Not a single eyewitness the commission heard saw the action in the way that the commission decided it had happened. All, without exception, were convinced that the President and Governor Connally were felled by two separate, wounding shots." Cook went onto argue that he considered the evidence linking Lee Harvey Oswald to the purchase of the weapon, to the same weapon discovered on the TSBD sixth floor, and the ballistics linking CE 399 to that weapon convincing: "To contend in the face of all this - and more besides - that Oswald was innocent is to endorse absurdity." However, he added that it was impossible for him to believe that Oswald acted alone.

The second part of the article, published on 20th June, was called Testimony of the Eyewitnesses . He argued that in spite of the speed with which Dallas authorities all but closed the case against Oswald, with a lone shooter, three-shots-fired theory, "a surprising number of spectators insisted with varying degrees of certainty that they had heard four, five or six shots." Cook went onto point out: "Exhibit 386, is a back view of the President's head and shoulders; it places the entry wound, not on a line with the tip of the shoulder; it places the entry wound, not on a line with the tip of the shoulder, not always in the middle of the back, but well above the shoulder level on the right side of the President's neck. In other words, the location of this wound has been changed!".

On 11th April, 1966, Nation Magazine published an article by Jacob Cohen, criticising the work of Cook and Edward Jay Epstein for not accepting the findings of the Warren Commission. This time there was no editorial disclaimer. Cook was furious with Carey McWilliams and insisted he ran his reply without deleting a single word, or he would never write for the magazine again. McWilliams agreed to do this and Cook's letter that appeared on 22nd August dismantled every point that Cohen had made.

It has been pointed out that about a third of Stout's FBI file is devoted to his 1965 novel, The Doorbell Rang. The novel concerns the publication of The FBI Nobody Knows (1964) by Fred J. Cook. In the novel, the wealthy Mrs. Rachel Bruner buys 10,000 copies of Cook's book and sends them to persons of influence, including cabinet members, Supreme Court justices, members of Congress and heads of corporations. Bruner believes that as a result of her actions she is being persecuted by the FBI and employs Nero Wolfe to investigate the organization.

Other books by Fred J. Cook included The Corrupted Land: The Social Morality of Modern Americans (1966), The Secret Rulers: Criminal Syndicates and How They Control the U.S. Underworld (1966), The Plot against the Patient (1967), What So Proudly We Hailed (1968), The Nightmare Decade: The Life and Times of Senator Joe McCarthy (1971), The Army-McCarthy Hearings (1971), The Rise of American Political Parties (1971), The Cuban Missile Crisis (1972), The Muckrakers: Crusading Journalists Who Changed America (1972), The U-2 Incident: An American Spy Plane Downed over Russia Intensifies the Cold War (1973), American Political Bosses and Machines (1973), The Pinkertons (1974), Lobbying in American Politics (1976), The Ku Klux Klan: America's Recurring Nightmare (1980), The Crimes of Watergate (1981), The Great Energy Scam: Private Billions vs. Public Good (1982) and Maverick: Fifty Years of Investigative Reporting (1984).

Fred J. Cook died on 4th April, 2003.