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New conviction

On 9 September 1899, the court rendered its verdict: Dreyfus was convicted of treason, but "with extenuating circumstances" (by five votes to two) and sentenced to ten years' imprisonment and a further degradation. Contrary to appearances, this verdict was on the verge of acquittal by one vote. The Code of Military Justice adopted the principle that a minority vote of three against four was an acquittal.

The day after the verdict, Alfred Dreyfus, after much hesitation, filed an appeal for a retrial. Waldeck-Rousseau, in a difficult position, tackled for the first time the possibility of a pardon. Dreyfus had to accept guilt. Exhausted, having been away from his family for too long, he accepted. The decree was signed by President Émile Loubet on 19 September 1899 and Dreyfus was released on 21 September 1899. Many Dreyfusards were frustrated by this final act. Public opinion welcomed this conclusion indifferently. France wanted civil peace and harmony on the eve of the Universal Exhibition of 1900 and before the big fight that the Republic was about to take for freedom of association and secularism.

It was in this spirit that on 17 November 1899, Waldeck-Rousseau filed an amnesty law covering "all criminal acts or misdemeanours related to the Dreyfus affair or that have been included in a prosecution for one of these acts" excluding only Alfred Dreyfus himself who was instead pardoned to be able to still seek acquittal. Many Dreyfusards protested as this indemnified not only Zola and Picquart against (further) punishment but also protected the real culprits. Despite these massive protests the bill was passed.