By order of Admiral Canaris the Vatican began to receive regular, detailed reports of the Nazi atrocities in Poland. The information had been gathered by agents of the Abwehr, who passed them on to Dr. Josef Müller, a devout Catholic and a leading figure in the Catholic resistance to Hitler - and Muller got the reports safely to Rome.
Canaris send one of his colleagues, Pastor Dietrich Bonhoeffer, on a flight to Sweden to meet secretly with Bishop Bell of Chichester. Bonhoeffer told Bell of the crimes his nation was committing, and assured Bell of growing resistance in Germany to such acts.
In March 1943, Canaris personally flied to Smolensk to plan Hitler's assassination with conspirators on the staff of the Army Group Center.
After World War 2 Canaris' efforts in trying to put a stop to the Nazi war crimes and genocide were revealed during the Nuremberg Trials.
In his great book Canaris the author Heinz Höhne tells how Canaris often helped those in need:
"He seldom dismissed an appeal for aid and comfort unless it seemed likely to provoke a head-on clash with the regime. Jews, in particular, had been snatched from mass destruction by many devious manoeuvres on his part. Thanks to him, numerous Jews or "half-Jews" wore Wehrmacht uniform or at least carried Abwehr papers guaranteeing them immunity from the Gestapo.
The rescue of five hundred Dutch Jews by Abwehrstelle den Haag in May 1941 .. would have been impossible without the Admiral's consent .. Even in late summer 1942 Canaris had mounted an audacious rescue operation by securing exit permits for twelve elderly Berlin Jews who had been represented to the Gestapo as Abwehr agents earmarked for use against he United states .."
In another instance he saved seven Jews from being sent to certain death by going personally to Himmler, complaining that Gestapo was arresting his agents. The seven were turned over to the Abwehr and taught a few codes, then smuggled out of Germany.
Among those who left Nazi-occupied territory thanks to Canaris was the archbishop of Krakow; a rabbi from Warsaw, who was able to immigrate to New York; and Madame Czimanska, the wife of the Polish military attaché in Berlin. Heinz Höhne tells how Canaris procured papers which enabled Madame Czimanska and her children to settle in Switzerland in the neighborhood of Berne, where she found an apartment which he sometimes visited on his subsequent trips to Switzerland. The Admiral also acted as a staging-post for correspondence between her and her mother in Warsaw.
Canaris appointed the anti-Nazi Hans Oster to the number two in the Abwehr agency. Oster contacted enemies of the Nazi regime and turned them into Abwehr agents - the most important were Hans Von Dohnanyi, the catholic lawyer Joseph Müller and Dietrich Bonhoeffer. All of Oster's actions were approved by Canaris, who actively supported the resistance.
Admiral Canaris, along with Oster, actually helped the Allies while supervising all German espionage and counterespionage. They were revealing important German strategy and battle plans to the Allies - from Hitler's impending western offensive against the Low countries and France to Hitler's plan to invade Britain. Canaris also misled Hitler into believing that the Allies would not land at Anzio in 1943.
April 1943 Canaris made contact with the former governor of Pennsylvania, Commander George H. Earle, Roosevelt's personal representative for the Balkans, stationed in Istanbul. One morning there was a knock on Earle's hotel room door and there stood - in civilian clothes - Admiral Wilhelm Canaris. He told Earle there were many sensible German people feeling that Hitler was leading their nation down a destructive path. Canaris continued that an honorable surrender from the German army to the American forces could be arranged.
Earle was convinced of the sincerity of the Admiral and immediately sent an urgent message to Washington via diplomatic pouch, requesting a prompt reply. A month later, Canaris phoned, as had been agreed, but Earle could only say "I am waiting for news, but have none today."
In the summer of 1943 Canaris met secretly with Stuart Menzies, Chief of British Intelligence, and William J. Donovan, head of the Office of Strategic Services, at Santander, Spain. Canaris presented Menzies and Donovan with his peace plan: a cease fire in the West, Hitler to be eliminated or handed over, and continuation of the War in the East. But though Donovan, Menzies and Canaris reached an agreement on the basis of Canaris' proposal, President Roosevelt flatly declined to negotiate with 'these East German Junkers' and called his presumptuous OSS chief to heel. Canaris' peace offer was rejected ..
That he was being misled by Canaris became evident to Adolf Hitler only after the conspirators attempted to kill him in July, 1944. Canaris was arrested and finally confined at Gestapo cellars at Prinz Albrechtstrasse, where he was kept in solitary confinement, and in chains.