The last days
That he was being misled by Canaris became evident to Adolf Hitler only after the conspirators attempted to kill him in July, 1944. Canaris and many others were arrested. The principal prisoners were finally confined at Gestapo cellars at Prinz Albrechtstrasse, where Canaris was kept in solitary confinement, and in chains.

In The Canaris Conspiracy Manvell and Fraenkel tell, how his cell door was permanently open, and the light burned continually, day and night. He was given only one third of the normal prison rations, and as the winter set in his starved body suffered cruelly from the cold. Occasionally he was humiliated by being forced to do menial jobs, such as scrubbing the prison floor, the SS-men mocking him.

On 7 February 1945 Canaris was brought to the Flossenburg concentration camp but he was still ill-treated and often endured having his face slapped by the SS guards. But for months Canaris baffled the SS-interrogators with one ruse after another, and he denied all personal complicity in the conspiracy. He never betrayed his fellow participants in the Resistance Movement.

In the closing days of World War II, in the gray morning hours of April 9, 1945, gallows were erected hastily in the courtyard. Wilhelm Canaris, pastor Dietrich Bonhoeffer, Major General Hans Oster, Judge Advocate General Carl Sack, Captain Ludwig Gehre - all were ordered to remove their clothing and were led down the steps under the trees to the secluded place of execution before hooting SS guards. Naked under the scaffold, they knelt for the last time to pray - they were hanged, their corpses left to rot.

Two weeks later the camp was liberated by American troops - on 23 April 1945.

One of Canaris' fellow-prisoners, the Danish Colonel Lunding, former Director of Danish Military Intelligence, was imprisoned in the cell next to Canaris. He had contact with Canaris shortly before he watched the naked figure of the Admiral being led to execution. Through tapping on the wall of his cell Canaris told him: "This is the end. Badly mishandled. My nose broken. I have done nothing against Germany. If you survive, please tell my wife .."  
Dietrich Bonhoeffer
The camp doctor, who had to witness the executions, remarked that he saw Bonhoeffer kneel and pray before being led to the gallows. He later recalled "I was most deeply moved by the way this lovable man prayed, so devout and so certain that God heard his prayer. At the place of execution, he again said a short prayer and then climbed the steps to the gallows, brave and composed. In the almost 50 years that I worked as a doctor, I have hardly ever seen a man die so entirely submissive to the will of God."
500 other suspected conspirators were executed at other camps that same day, among them the leading administrator in the resistance and its legal adviser, Hans von Dohnanyi, at Sachsenhausen.
During the waning weeks of the Nazi era, SS Obersturmbannführer Walter Huppenkothen, born 1909,  and Sturmbannführer Otto Thorbeck, born 1911, had been detailed to the Flossenburg concentration camp to eliminate Canaris and the other resistance figures. The SS men staged a bogus "trial" before their men hung the victims.
After the war Huppenkothen and Thorbeck stood trial on three occasions, but the courts were never able to satisfactorily dispose of their case.
In 1956 the German High Court ruled that this ceremony had been enough to render the murders "legal." The high court judges also held that the killings were "legal" because the Nazi regime had possessed the right to execute "traitors." The court, in effect, reconvicted the victims.

Adolf Hitler had founded the Third Reich 12 years and three months before the nightmare was over. His Nazi Regime led to the annihilation of more than six million Jews in Europe. The Third Reich would survive him for one week ...

After the war major general Erwin Lahousen, formerly on Admiral Canaris' staff, said that his chief 'hated Hitler, his system and his methods. He hated war. He was a human being.'

One of Canaris' friends, Hans Bernd Gisevius, tells about the Admiral in his book from 1947 To the Bitter End:

"Canaris hated not only Hitler and Himmler, but the entire Nazi system as a political phenomenon .. He was everywhere and nowhere at once. Everywhere he traveled, at home and abroad and to the front, he always left a whirl of confusion behind him .. In reality this small, frail, and somewhat timid man was a vibrating bundle of nerves. Extremely well read, oversensitive, Canaris was an outsider in every respect. In bearing and manner of work he was the most unmilitary of persons .."

Admiral Wilhelm Canaris

"I die for my fatherland. I have a clear conscience. I only did my duty to my country when I tried to oppose the criminal folly of Hitler" - Admiral Wilhelm Canaris