The subsequent court-martial was notable for numerous errors of procedure. For instance, the defense was unaware of a secret dossier which the prosecution had provided to the military judges. The withholding of this dossier was illegal. As to the initial "why" of the case, the renowned French military historian Jean Doise provides detailed evidence that Dreyfus was used as a patsy or scapegoat through manipulations by French military counter-intelligence (the so-called Bureau de Statistique led by Lt Colonel Sandherr). The purpose of the manipulations was to help convince Germany that the new French field gun was the imperfect, soon-to-be terminated Baquet project listed in the bordereau, instead of the revolutionary French 75mm field gun which was developed in great secrecy at the very same time (1892-1896).

The torn up bordereau found discarded in the waste paper basket of Attaché von Schwartzkoppen was, in fact, a fabrication which had been hand written and delivered by a French-born infantry officer of Hungarian descent, Major Ferdinand Walsin Esterhazy. The latter either hoped to extract money from the German Attaché or was, as proposed by Jean Doise, planting a deception in German hands to throw them off the secret 75mm field gun project. The latter explanation fits with the fact that Esterhazy, in spite of being exposed by Colonel Picquart as the real author of the bordereau, was acquitted by French military Justice in January 1898 and let go to retire in England with a pension. Furthermore, and as also proved by the archival records, Walsin-Esterhazy had once been working full-time as a lieutenant on the staff of military counter-intelligence. This episode took place during the early part of Esterhazy's career, before the Dreyfus Affair. In other words and in clear terms, there is verifiable evidence that Major Esterhazy was a past member of the Sandherr counter-intelligence network. Alfred Dreyfus was put on trial in 1894 and was accused of espionage, found guilty and sentenced to life in prison on Devil's Island. He was publicly cashiered: his rank marks and buttons were ripped off his uniform and his sabre was broken. In June 1899 the case was reopened, following the uncovering of exonerating evidence and of the fact that Dreyfus had been denied due process during the initial court-martial. France's Court of Cassation quashed his conviction and ordered a new court-martial. Despite the new evidence presented at his new military trial, Dreyfus was reconvicted in September and sentenced to 10 years in prison. He was subsequently pardoned by President Émile Loubet and freed, but would not be formally exonerated until 12 July 1906, when the Court of Cassation annulled his second conviction. He was thereafter readmitted to the army and made a knight in the Légion d’Honneur. Dreyfus was recalled to active duty and served behind the lines of the Western Front during World War I as a Lieutenant-Colonel of Artillery though he did perform some frontline duties in 1917. He served his nation with distinction beyond his natural retirement age.