The bisthum of Würzburg had been a German country governed by the Catholic church for a long time.
Since the Sacco di Roma however, pilgrims returning from Rome with the bad news had spread discontent in Germany. The break came in 1475: When king Heinrich VIII secularized and annexed the bistums of Augsburg and Trient for his lands, the HRE fell into a kind of Civil War. All the princes tried to annex the clerical lands, which leads to lots of confusion and little wars for said lands, which are subsumed as the Twenty-Year War.
In the same year, in the bisthums of Würzburg and Münster, millenialist sects took the power, declared the Gottesfreistaat (God's republic - another kind of theocracy). The latter ones even managed to extend their lands during the chaos of the war, deposing some small princes of NW Germany. Both states ignored the HRE and its emperor for their concerns.
When the war was over, however, the German princes remembered the Gottesfreistaaten again. During the reforms of the HRE (1500-08), the Gottesfreistaaten of Münster and Würzburg were put into Reichsacht (meaning: everyone was officially allowed kill their people and take their lands).
While Münster would continue for longer and even could expand its territory, Würzburg wasn't that lucky: In 1545, burgrave Johann II von Hohenzollern of Ansbach and Bayreuth defeated the Gottesfreistaat and annexed it, thus forming the new duchy of Franconia. For this deed, the emperor promised him to support his claims for Pomerania too. Later uprisings of the people were defeated soon, and they either had to emigrate or accept their fate.
Note that Würzburg was named after its capital Würzburg.
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