Apor played a leading role in the Hungarian episcopal assembly through his whole-hearted rejection of the anti-Jewish measures introduced by the government, and especially after the German takeover of the country in March 1944. As president since 1943 of the Holy Cross Society established to protect baptized Jews, he understandably displayed a particular concern for the members of his flock. He nevertheless condemned without reservation any legal discrimination based on racial theory. When the civil authorities ordered everyone considered Jewish to move into the newly-formed local ghettos, Apor openly pilloried from the pulpit those who claimed that there were people, groups or races that could be hated or tortured. To deprive innocent people of their freedom and civic rights was a flagrant denial of human and divine justice. He firmly remonstrated with the minister for home affairs, and when a priest sent by him to offer solace to Jews was refused entry to the ghetto by the police, he wrote to the prime minister and personally appproached the local Gestapo. When told that they were simply obeying Hitler's orders, Apor retorted: "Tell the Führer that the divine law of justice is obligatory even for him." Obviously all his efforts were of no avail.
After news from Auschwitz had reached the bishops, Apor — who had privileged information, his brother being Hungarian ambassador to the Vatican and his sister the head of the Hungarian Red Cross — urged the primate, Cardinal Serédi, to issue a pastoral letter condemning the persecution of the Jews. As the primate was dilly-dallying — he feared that such an intervention might engender increased cruelty and even endanger the Church — Apor wrote three further letters to the cardinal, pressing him to send an ultimatum to the government. Finally, by the end of June 1944 the letter was ready and was printed. But the plan was reported to the authorities (by Serédi?) and predictably its distribution was forbidden, so that it was never read in the churches.
By April 1945 Soviet troops were besieging Győr. Apor generously offered shelter to a large number of frightened civilians in the cellars of the bishop's castle. On Good Friday, April 30, a group of drunken Russian soldiers burst into the episcopal residence looking for women. With noble courage, the bishop confronted them and ordered them to get out. One of the soldiers shot him three times and they all ran away. He died a martyr three days later on May 3, but the women were saved.
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