One Library, however, was violently opposed: the Archives of Freemasonry. Marshal Petain considered freemasonry to be a state within the State, an international network in communication with the German masonic lodges. He ordered the closure of all lodges in France and turned the cataloguing of their archives over to a team from the Bibliothèque Nationale. Anti-masonic laws were enacted and remained in effect for nearly three years, the identité of high-ranking freemasons - well known before the war - was published in the Journal Officiel, and the contents of its archives published under the title Documents Maçonniques.
When Pierre Laval returned to power as prime minister in 1942, he re-established the lodges and relieved Bernard Faÿ of his responsability within the Vichy gouvernement's Secret Society Service. Faÿ received the following threat from « The ritual sacrifice : you wished to destroy freemasonry by revealing its secrets to the sacrilegious curiosity of the uninitiated, your days are numbered! ».
On the very day of the Liberation, two police officers stormed Faÿ’s office in the rue de Richelieu and threw him in prison. At Fresnes, at la Santé then at Drancy; he was interrogated by a freemason police inspector, Mr Le Poittevin, who attempted to bring a death-penalty charge against him, alleging that Faÿ had been in communication with the Germans, played a political role during the war, and was an Antisemite. He rebutted each allegation point by point, but his fate was already sealed.
During the trial on secret societies at the special tribunal in december 1946, his attorney Maître Chresteil tried in vain to present favorable testimony from witnesses on his behalf in order to prove that the allegations against Faÿ were based on passion and vengeance rather than concrete evidence. The trial was held amidst a post-liberation atmosphere of « settling the score » and was attended by a crowd of militant communists, members of the gutter press and those who had waited to the last minute to join the Resistance.
Bernard Faÿ narrowly escaped the death penalty, but was sentenced to a lifetime of hard labor as well as having all his possessions confiscated. He was further humiliated by being named « National Disgrace », a title récent created by General de Gaulle. After sentencing, the tribunal adjourned rapidly, with no possibility of appeal.
Faÿ was incarcerated as a political prisoner in the prison of Saint Martin de Ré and then at Fontevraud penitentiary. Several petitions for pardons were submitted on his behalf, but then blocked, even though President Vincent Auriol and many in his circle were favorably disposed towards granting his freedom. At the end of seven years in prison, with no hope of regaining his liberty through legal channels - and even of saving his own life, since he was gravely ill - while being transferred to a hospital in Angers, he managed to escape. He fled to Fribourg in Switzerland, where he awaited a free medical pardon from President Coty, which was signed by the then Minister of Justice, François Mitterrand. His previously confiscated possessions were returned (though many had been sold) and the title of National Disgrace cancelled. He returned home in 1957 and continued his work as an historian.