Largely by bribing diplomats, Weissmandl was able to smuggle letters to people he hoped would help save the Jews of Europe, alerting them to the progressive Nazi destruction of European Jewry. It is known that he managed to send letters to Winston Churchill and Franklin D. Roosevelt, and he entrusted a diplomat to deliver a letter to the Vatican for Pope Pius XII.
He also begged the Allies to bomb the rails leading to Auschwitz, but to no avail. He believed that if the Hungarian Jews would resist, then only a small number of them would be deported, as the Germans in 1944 couldn't garner enough soldiers to leave the front and deal with the Jews simultaneously. Of around 900,000 Hungarian-speaking Jews, close to 600,000 were murdered.
Weissmandl was a scholar and an expert at deciphering ancient manuscripts. In order to carry out his research of these manuscripts, he traveled to the Bodleian Library in Oxford, England. It is related that he was treated with great respect by the Chief Librarian of the Bodleian after an episode when he correctly identified the author of a manuscript which had been misattributed by the library’s scholars.
During the period of WWII, Weissmandl lead the Working Group of Bratislava together with Gisi Fleischmann (see the next section). In 1944, Weissmandl and his family were put on a train headed for Auschwitz. Rabbi Weissmandl escaped from the sealed train by sawing open the lock of the carriage with an emery wire he had secreted in a loaf of bread. He jumped from the moving train, breaking his leg in the process, and hid in a secret bunker in suburban Bratislava.
Rudolf Kasztner and his Nazi associate Kurt Becher took Weissmandl from his Bratislava bunker to Switzerland. This was highly unusual for both Kasztner and Becher. There is some speculation that Kasztner and Becher sought to reinforce their alibis for the predictable post-war trials.
When the Nazis, aided by members of the puppet Slovak government, began its moves against the Slovakian Jews in 1942, members of the Slovak Judenrat formed an underground organization called the Working Group. It was led by Gisi Fleischmann and Rabbi Weissmandl. The group's main activity was to help Jews inasmuch as possible in part through payment of large bribes to German and Slovak officials. Already in 1942 the Working Group initiated high level ransom negotiations with the Germans (ref. Fuchs and Kranzler book). The transportation of Jews was in fact halted for a long time after they arranged a $50,000 (in 1952 dollars) ransom deal with the Nazi official Dieter Wisliceny. The Working Group was also responsible for the ambitious but ill-fated Europa Plan which would have seen large numbers of European Jews "bought" from their Nazi captors. On the order of one to two million dollars ransom was required to stop most transports in late 1942, and the Germans asked for a 10% initial down payment. The down payment was never made, due to lack of funds. (Ref. David Kranzler's Thy Brother's Blood and Abraham Fuchs' The Unheeded Cry.)
Since the business of the Working Group required a continuous supply of large sums of money, they turned to the international Jewish organizations for help, via their representatives in Switzerland. Weissmandl claimed that too little money was provided too late and that this was due to the indifference of those he asked. Specifically, he accused the Zionist organizations of refusing to assist in saving Jews unless they were to go to Palestine (a condition the Nazis were unwilling to accept). Weissmandl supported his allegations by quoting letters from memory, and some historians such as Bauer had doubt in the accuracy of his account. Other historians, such as Fuchs and Kranzler, accepted Rabbi Weissmandl's word. Nonetheless, some of these letters have been later found, and when compared to Rabbi Weissmandl's account, they are very similar, if not word-for-word in some instances.
After the war, Weissmandl arrived in the United States having lost his family and having been unable to save Slovakian Jewry. At first he was so distraught that he would pound the walls and cry bitterly on what had befallen his people. Later he remarried and had children, but was unable to overcome his grief. Although Rabbi Weissmandl remarried and fathered five children, he never forgot his family in Europe and suffered from depression his entire life because of the Holocaust.
In November of 1946, Weissmandl and his brother-in-law, Rabbi Sholom Moshe Ungar, re-established the Nitra Yeshiva in Somerville, New Jersey , gathering surviving students from the original Nitra Yeshiva. With the help of Rabbi Shraga Feivel Mendlowitz, Rabbi Weissmandl a year later bought the Brewster estate in Mount Kisco, in Westchester County, New York and moved his Yeshiva there. There he established a self-sustaining agricultural community known as the "Yeshiva Farm Settlement". At first this settlement wasn't welcome by its neighbors, but in a town hall meeting, Helen Bruce Baldwin (1907-1994) of nearby Chappaqua, wife of New York Times military correspondent and Pullitzer Prize winner, Hanson W. Baldwin; impressed by Rabbi Weissmandl, defended its establishment and wrote a letter-to-the-editor to the New York Times regarding it. Weissmandl designed the community's yeshiva to conform with Talmudic accounts of agricultural settlements, where a man would study Torah continuously until an age suitable for marriage, whereupon he would farm during the day and study in the evenings. While this novel approach was not fully realized, the yeshiva flourished. Currently, the settlement is known as the Nitra community.
Weissmandl pioneered the modern search for hidden codes in the Torah. As a student, he copied large portions of the Torah onto ten characters by ten character grids. He thereby set the stage for the controversial, computer-based generation of Bible Codes since the 1980s.
In a letter, dated May 15th, 1944, addressed to the Zionist leadership in Palestine (under British rule) Rabbi Weissmandl called on the Zionist leadership to take stronger action on behalf of European Jewry which was systematically being destroyed by the Nazi lead genocide: "And you - our brothers in Palestine, in all the countries of freedom, and you, ministers of all the kingdom - how do you keep silent in the face of this great murder ? Silent while thousand on thousands, reaching now to six million Jews, were murdered. And silent now while tens of thousands are still being murdered and waiting to be murdered? Their destroyed hearts cry to you for help as they bewail your cruelty. Brutal you are and murderers too you are, because of the cold-bloodedness of the silence in which you watch.
Two of Weissmandl's books were published posthumously.
In 1958, Rabbi Weissmandl republished the magnum opus of Rabbi Jonah Teomim-Frankel, Kikayon D'Yonah with his own footnotes and glosses. In the introduction to this volume, Rabbi Weissmandl gives an emotional history lesson.