He retained his position in May 1894 in the Cabinet of Dupuy, which probably gave him the notion of being indispensable: "He cut short everyone, dry, haughty, a provocative self-conceit, infallible and sure of his destiny.
"[2] In August 1894, Mercier conditionally released a person which earned him a campaign from the right-wing press who accused him of covering up for "Jews and spies."
From 7 October 1894, convinced who was the guilty party solely on the basis of the dubious expertise in handwriting of Alphonse Bertillon, Mercier decided on the guilt of Dreyfus.
In J'accuse ...!, Émile Zola did not understand the importance of Mercier's role and accused him simply of "aiding and abetting, at least through weakness of mind, one of the largest iniquities of the century.
[6]" Summonsed in the Zola trial in February, "haughty, impassive, precise, disdainfully entrenched in the consciousness of his own infallibility, he declared that Dreyfus was a traitor who had been justly and lawfully convicted"[7] and refused to answer on the existence of secret documents.
Questioned in November 1898 by the Criminal Chamber of the Supreme Court, in the context of the proceedings for review of the 1894 trial, Mercier reaffirmed the guilt of Dreyfus.
He announced that there would be decisive revelations to come in the nationalist press, as the existence of an original copy of the bordereau annotated by the Kaiser (Wilhelm II of Germany).
His testimony before the Military Court brought no new revelations, and he declared: My conviction since 1894 has not suffered the slightest damage, rather it is deepened by a more comprehensive study of the case, it is finally strengthened by the failure of the results obtained [from the Military Court] to demonstrate the innocence of the convicted, despite the huge number of millions spent foolishly…At the end of 1899, an amnesty law was passed by Parliament, against the fierce opposition of Georges Clemenceau and Jean Jaurès.
On the eve of the judgment without reference by the Supreme Court, he was unable to provide any "irrefutable" evidence despite the pleas of the anti-Semitic press and the nationalists.
On 29 June 1907, before 6000 people at the Salle Wagram, French Action gave him a gold medal in memory of the session in which he had "stood up to the parliamentary madness."