There were two aspects that made the life of Rabbi Yonasan Eibeschutz memorable. The first was his tremendous scholarship in Torah; “nigleh” (the open, revealed Torah of the Bible and the Talmud) and “nistar” [the hidden, esoteric Torah of the “Zohar” and the “Kabbalah”] The second was a tragic dispute that he had with Rabbi Yaakov Emden, in the wake of the catastrophic episode that nearly tore the Jewish world apart, the rise and fall of the false-Messiah, Shabbetai Tzvi.
An “illui,” a child prodigy in his youth, Rabbi Yonasan became one of the great commentators on the Talmud and on the “Shulchan Aruch,” the Codes of Jewish Law. At the age of twenty-one, he headed the “Yeshiva” (Talmudic Academy) of Prague, and his oratorical abilities were already known far and wide. Somewhat unusually, he also interacted with priests and with the Cardinal in the area, debating religious topics with them. This Cardinal allowed him to print a copy of the Talmud, with passages critical of Christianity censored out. This aroused the hostility of the other rabbis of Prague, and also lent an air of controversy to Rabbi Yonasan. However, in 1725, he was among the Prague rabbis who put the followers of Shabbetai Tzvi in “cherem” (excommunication).
As noted above, Rabbi Yonasan was highly proficient in “Kabbalah,” and he wrote amulets for many Jews who wanted them for their mystical powers. Rabbi Yaakov Emden, also a great Torah scholar, had dedicated himself to the uprooting of any remnant of support for Shabbetai Tzvi. He also had sharply criticized the Ramchal (Rabbi Moshe Chaim Luzzatto), not for any connection with Shabbateanism but for what he considered abuse of his knowledge of “Kabbalah.” We see that Rabbi Yaakov Emden possessed a critical personality, although that can be very easily understood in the light of the disaster that had just befallen the Jews and their false Messiah.
In any case, Rabbi Yaakov Emden came into possession of one of the amulets written by Rabbi Yonasan Eibeschutz and he claimed that he found in it evidence of Shabbateanism. Rabbi Eibeschutz vigorously denied the charge and enlisted in his support great rabbis such as the “Noda BiYehudah,” Rabbi Yechezkel Landau and Rabbi Eliyahu, the Gaon of Vilna. But Rabbi Yaakov Emden also received significant rabbinical support and the controversy became so intense that it came to the attention of the Emperor Frederick of Denmark. The Emperor first sided with Rabbi Yaakov Emden, and deposed Rabbi Yonasan Eibeschutz, but later reversed himself, and restored Rabbi Eibeschutz to his position as a leader of the Jewish Community.
This great internal dispute between two Torah giants was one of the bitter consequences of the Shabbetai Tzvi fiasco. It is also quite likely that the fierce opposition of the Vilna Gaon and other “Mitnagdim” (Those in Opposition) to Chassidut, a new mass spiritual movement that arose around that time, initiated by the Baal Shem Tov, that put its emphasis on “Kabbalah” and Prayer, rather than exclusive focus on the study of Talmud, developed as a consequence of the Shabbetai Tzvi disaster, and this hostility has lasted for hundreds of years, albeit with continually lessening intensity, till today.