The accession of Paul III to the Papal throne revived all counter reformatory activity was revived. Born Alessandro Farnese, the Italian, who took the regnal name of Paul was both shrewd and ruthless. He worked swiftly to reassert papal control over Christendom as the Reformation made significant inroads into Catholic strongholds. 

Paul III began by convene a church council where he proposed to clearly define church doctrine. He also overcame political and beaureaucratric obstacled within the church to implement reform in areas where abuse and exploitation were the worst. His most forceful measure against the Reformation was launching a militant counter offensive against Protestantism with the help of staunch Catholic allies like the King of Spain and the powerful Guise family of France. 

Paul III resurrecuted the largely defunct Roman Inquisition which had been out of commission since the 13th century. The Inquisition, also known as the Holy Office, was an ecclesiastical circuit court whose officers and judges apphrehended, tried and sentenced heretics throughout Christendom. 

The Pope also appointed counter-reform minded cardinals to the College of Cardinals to ensure that future Popes would continue his efforts. But perhaps the most important counter-reformatory measure he implemented was convening the Council of Trent. 

The Council of Trent was held in Siwtzerland, a particularly ironic location given early support for the Reformation in cities like Zurich and Geneva. The Council of Trent focused primarily on clearly defining Catholic doctrine, marking out the divergence between newly emerging Protestant theology and traditional Catholic theology. Trent placed Catholicism in a position to mount a serious militant counteroffensive against Protesant and Protestantism. 

The church refused to compromise or temporised any of its doctrinal stances, instead using Trent as a vehicle to emphasize traditional Catholic theology. Some of the most pointed assertions Trent emphaised were the authority of the councils and traditions of the church, placing them on equal footing with Scriptures, the necessity of good works to salvation and the importance of all seven sacraments as channels of grace and not mere symbols. Transubstationation was upheld and the power of the preiusts to enact the miracle of the mass was reasserted as was the special position of the priesthood. It also condemend the stripped-down Protestant services, asserting that the ritual and ceremony of the church were essential elements of proper worship. 

Trent created an atmosphere of militant Catholicism bent on destroying all facets of the encroaching Protestant Reformation. To this end the church relied on three main weapons. First the Inquisition was used to execute thousands of Protestants especially in Germany and The Netherlands. 

Second the church introduced The Index of Forbidden Books, a long list of proscribed Protestant literature. All those who read work from this list were condemned to eternal damnation. 

The final facet of the militant counter-Reformnation was the deployment of the Jesuits, a militant new religious order that was tasked with providing foot soldiers in the new holy war the church had begun to wage.