structural:expansion
Securing the Protestant Reformation (1553–1555)

After the death of Servetus, Calvin was acclaimed a defender of Christianity, but his ultimate triumph over the libertines was still two years away. He had always insisted that the Consistory retain the power of excommunication, despite the council's past decision to take it away. During Servetus's trial, Philibert Berthelier asked the council for permission to take communion, as he had been excommunicated the previous year for insulting a minister. Calvin protested that the council did not have the legal authority to overturn Berthelier's excommunication. Unsure of how the council would rule, he hinted in a sermon on 3 September 1553 that he might be dismissed by the authorities. The council decided to re-examine the Ordonnances and on 18 September it voted in support of Calvin—excommunication was within the jurisdiction of the Consistory. Berthelier applied for reinstatement to another Genevan administrative assembly, the Deux Cents (Two Hundred), in November. This body reversed the council's decision and stated that the final arbiter concerning excommunication should be the council. The ministers continued to protest, and as in the case of Servetus, the opinions of the Swiss churches were sought. The affair dragged on through 1554. Finally, on 22 January 1555, the council announced the decision of the Swiss churches: the original Ordonnances were to be kept and the Consistory was to regain its official powers.

The libertines' downfall began with the February 1555 elections. By then, many of the French refugees had been granted citizenship and with their support, Calvin's partisans elected the majority of the syndics and the councilors. On 16 May the libertines took to the streets in a drunken protest and attempted to burn down a house that was supposedly full of Frenchmen. The syndic Henri Aulbert tried to intervene, carrying with him the baton of office that symbolized his power. Perrin seized the baton and waved it over the crowd, which gave the appearance that he was taking power and initiating a coup d'état. The insurrection was soon over when another syndic appeared and ordered Perrin to go with him to the town hall. Perrin and other leaders were forced to flee the city. With the approval of Calvin, the other plotters who remained in the city were found and executed. The opposition to Calvin's church polity came to an end.